Steps to reproduce -
1. Create a Jenkins slave node.
2. Specify the "Remote FS Root" value of the slave as a relative path.
3. Use any auto-install tool, for example Ant (by adding Ant Installation settings in Jenkins configuration)
4. Run a build with "Invoke Ant" task. This task should use the version of Ant setup in the Ant-Installation settings.
5. Build fails as it is unable to find the recently downloaded ant binary.

Sample Build Output -

Started by user anonymous
Building remotely on Test Node in workspace Documents/jar_sources/workspace/Test MATT Plugin
Unpacking http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.0-bin.zip to Documents/jar_sources/tools/hudson.tasks.Ant_AntInstallation/ant-test on Test Node
[Test MATT Plugin] $ Documents/jar_sources/tools/hudson.tasks.Ant_AntInstallation/ant-test/bin/ant clean
FATAL: command execution failed.
java.io.IOException: Cannot run program "Documents/jar_sources/tools/hudson.tasks.Ant_AntInstallation/ant-test/bin/ant" (in directory "Documents/jar_sources/workspace/Test MATT Plugin"): error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at hudson.Proc$LocalProc.<init>(Proc.java:244)
at hudson.Proc$LocalProc.<init>(Proc.java:216)
at hudson.Launcher$LocalLauncher.launch(Launcher.java:763)
at hudson.Launcher$ProcStarter.start(Launcher.java:353)
at hudson.Launcher$RemoteLaunchCallable.call(Launcher.java:988)
at hudson.Launcher$RemoteLaunchCallable.call(Launcher.java:955)
at hudson.remoting.UserRequest.perform(UserRequest.java:118)
at hudson.remoting.UserRequest.perform(UserRequest.java:48)
at hudson.remoting.Request$2.run(Request.java:326)
at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:53)
at java.lang.ProcessImpl.start(ProcessImpl.java:91)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 15 more
Build step 'Invoke Ant' marked build as failure
Finished: FAILURE