First, apologies in advance, as I might be filing this issue in the wrong component and/or hopefully there's a potential workaround or better way of working through this.

Since upgrading the Managed Script Plugin and Config File Provider Plugin (and a few others) to the latest versions - 1.3 and 2.15.1, respectively, we're seeing the following bustage:

1. With our current configuration, whenever we load our non-Pipeline jobs' /configure pages, we get HTTP 500s in:

• fillFileIdItems
• fillBuildStepIdItems
• descriptorByName/org.jenkinsci.plugins.managedscripts.ScriptBuildStep/checkBuildStepId?value=org.jenkinsci.plugins.managedscripts.ScriptConfig1429801884194&buildStepId=org.jenkinsci.plugins.managedscripts.ScriptConfig1429801884194

2. This presents itself as "ERROR" links in the "Execute managed script" sections of our "Build" portion in the job's config.
3. Clicking on "view selected script" in the screenshot yields a 404 for that script.
4. The stack trace/exception for the 2nd managed-script's error looks like this:

javax.servlet.ServletException: java.lang.IllegalStateException
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:796)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.MetaClass$5.doDispatch(MetaClass.java:236)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:58)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.MetaClass$5.doDispatch(MetaClass.java:236)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:58)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:649)
at org.kohsuke.stapler.Stapler.service(Stapler.java:238)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:812)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1669)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:135)
at org.jenkinsci.plugins.ssegateway.Endpoint$SSEListenChannelFilter.doFilter(Endpoint.java:206)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at com.cloudbees.jenkins.support.slowrequest.SlowRequestFilter.doFilter(SlowRequestFilter.java:37)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at com.smartcodeltd.jenkinsci.plugin.assetbundler.filters.LessCSS.doFilter(LessCSS.java:47)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at io.jenkins.blueocean.ResourceCacheControl.doFilter(ResourceCacheControl.java:134)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:201)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:178)
at net.bull.javamelody.PluginMonitoringFilter.doFilter(PluginMonitoringFilter.java:85)
at org.jvnet.hudson.plugins.monitoring.HudsonMonitoringFilter.doFilter(HudsonMonitoringFilter.java:104)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at hudson.plugins.greenballs.GreenBallFilter.doFilter(GreenBallFilter.java:59)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at jenkins.metrics.impl.MetricsFilter.doFilter(MetricsFilter.java:125)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at hudson.util.PluginServletFilter.doFilter(PluginServletFilter.java:126)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at hudson.security.csrf.CrumbFilter.doFilter(CrumbFilter.java:86)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:84)
at hudson.security.UnwrapSecurityExceptionFilter.doFilter(UnwrapSecurityExceptionFilter.java:51)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:117)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.providers.anonymous.AnonymousProcessingFilter.doFilter(AnonymousProcessingFilter.java:125)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.rememberme.RememberMeProcessingFilter.doFilter(RememberMeProcessingFilter.java:142)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:271)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.BasicHeaderProcessor.doFilter(BasicHeaderProcessor.java:93)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:249)
at hudson.security.HttpSessionContextIntegrationFilter2.doFilter(HttpSessionContextIntegrationFilter2.java:67)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at hudson.security.ChainedServletFilter.doFilter(ChainedServletFilter.java:76)
at hudson.security.HudsonFilter.doFilter(HudsonFilter.java:171)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.kohsuke.stapler.compression.CompressionFilter.doFilter(CompressionFilter.java:49)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:82)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.kohsuke.stapler.DiagnosticThreadNameFilter.doFilter(DiagnosticThreadNameFilter.java:30)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:553)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
at org.eclipse.jetty.server.Server.handle(Server.java:499)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:311)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257)
at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:544)
at winstone.BoundedExecutorService$1.run(BoundedExecutorService.java:77)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException
at org.jenkinsci.plugins.configfiles.GlobalConfigFiles.get(GlobalConfigFiles.java:32)
at org.jenkinsci.plugins.configfiles.ConfigFiles.getByIdOrNull(ConfigFiles.java:87)
at org.jenkinsci.plugins.managedscripts.ScriptBuildStep$DescriptorImpl.doCheckBuildStepId(ScriptBuildStep.java:305)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.kohsuke.stapler.Function$InstanceFunction.invoke(Function.java:335)
at org.kohsuke.stapler.Function.bindAndInvoke(Function.java:175)
at org.kohsuke.stapler.Function.bindAndInvokeAndServeResponse(Function.java:108)
at org.kohsuke.stapler.MetaClass$1.doDispatch(MetaClass.java:124)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:58)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
... 79 more