More info. Here is what the build slave log has for that job:
Aug 23, 2012 12:38:49 PM hudson.plugins.doxygen.DoxygenDirectoryParser getDoxyge
nGeneratedDir
INFO: Created filepath with the following path:/home/builduser/workspace/job/build/html
Failed to load native POSIX impl; falling back on Java impl. Stacktrace follows.
java.lang.UnsatisfiedLinkError: Unable to load library 'libc.so.6': com.sun.jna.
Native.open(Ljava/lang/String;)J
at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:166)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:239)
at com.sun.jna.Library$Handler.<init>(Library.java:140)
at com.sun.jna.Native.loadLibrary(Native.java:366)
at org.jruby.ext.posix.POSIXFactory.loadLibC(POSIXFactory.java:96)
at org.jruby.ext.posix.POSIXFactory.loadLinuxPOSIX(POSIXFactory.java:65)
at org.jruby.ext.posix.POSIXFactory.getPOSIX(POSIXFactory.java:24)
at hudson.os.PosixAPI.<clinit>(PosixAPI.java:40)
at hudson.Util.resolveSymlink(Util.java:1067)
at hudson.Util.resolveSymlink(Util.java:1030)
at hudson.util.DirScanner$Glob.scan(DirScanner.java:115)
at hudson.FilePath.writeToTar(FilePath.java:1820)
at hudson.FilePath.access$1000(FilePath.java:166)
at hudson.FilePath$36.invoke(FilePath.java:1761)
at hudson.FilePath$36.invoke(FilePath.java:1758)
at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2193)
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:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:636)
Aug 23, 2012 1:29:03 PM hudson.plugins.doxygen.DoxygenDirectoryParser retrieveDoxygenDirectoryFromDoxyfile
INFO: Using the Doxyfile information.
Aug 23, 2012 1:29:03 PM hudson.plugins.doxygen.DoxygenDirectoryParser loadDoxyFile
INFO: The Doxyfile path is 'file:/home/builduser/workspace/job/build/Doxyfile'.
This build job with the failing Doxygen call works fine on the old Jenkins server but fails on the new server even with the job actually running on a build slave.