Cannot authenticate anymore using Unix security realm after upgrading to Ubuntu from Maverick to Natty.
This one's probably due to JNA 3.2.4 incompatibility with Natty. Has already been reported : http://java.net/jira/browse/JNA-184

SEVERE: Servlet.service() for servlet Stapler threw exception
java.lang.UnsatisfiedLinkError: Unable to load library 'pam': libpam.so: cannot open shared object file: No such file or directory
at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:164)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:237)
at com.sun.jna.Library$Handler.<init>(Library.java:140)
at com.sun.jna.Native.loadLibrary(Native.java:374)
at com.sun.jna.Native.loadLibrary(Native.java:359)
at org.jvnet.libpam.impl.PAMLibrary.<clinit>(PAMLibrary.java:132)
at sun.misc.Unsafe.ensureClassInitialized(Native Method)
at sun.reflect.UnsafeFieldAccessorFactory.newFieldAccessor(UnsafeFieldAccessorFactory.java:43)
at sun.reflect.ReflectionFactory.newFieldAccessor(ReflectionFactory.java:140)
at java.lang.reflect.Field.acquireFieldAccessor(Field.java:936)
at java.lang.reflect.Field.getFieldAccessor(Field.java:917)
at java.lang.reflect.Field.get(Field.java:376)
at com.sun.jna.Native.loadLibraryInstance(Native.java:398)
at com.sun.jna.Native.getStructureAlignment(Native.java:507)
at com.sun.jna.Structure.setAlignType(Structure.java:191)
at com.sun.jna.Structure.<init>(Structure.java:149)
at com.sun.jna.Structure.<init>(Structure.java:145)
at com.sun.jna.Structure.<init>(Structure.java:141)
at com.sun.jna.Structure.<init>(Structure.java:132)
at org.jvnet.libpam.impl.PAMLibrary$pam_conv.<init>(PAMLibrary.java:107)
at org.jvnet.libpam.PAM.<init>(PAM.java:73)
at hudson.security.PAMSecurityRealm$PAMAuthenticationProvider.authenticate(PAMSecurityRealm.java:91)
at org.acegisecurity.providers.ProviderManager.doAuthentication(ProviderManager.java:195)
at org.acegisecurity.AbstractAuthenticationManager.authenticate(AbstractAuthenticationManager.java:45)
at org.acegisecurity.ui.webapp.AuthenticationProcessingFilter.attemptAuthentication(AuthenticationProcessingFilter.java:71)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:252)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.basicauth.BasicProcessingFilter.doFilter(BasicProcessingFilter.java:173)
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:66)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at hudson.security.ChainedServletFilter.doFilter(ChainedServletFilter.java:76)
at hudson.security.HudsonFilter.doFilter(HudsonFilter.java:164)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:81)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at org.apache.coyote.ajp.AjpAprProcessor.process(AjpAprProcessor.java:427)
at org.apache.coyote.ajp.AjpAprProtocol$AjpConnectionHandler.process(AjpAprProtocol.java:384)
at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1584)
at java.lang.Thread.run(Thread.java:679)