_jrubyvars.bat batch is broken on windows, it does not only add the jars in jruby/lib directory but all jars located in sub directories.
this is inconsistent with unix platforms and create issues with glassfish v3 integration.
if you replace
for /r "%JRUBY_HOME%\lib" %%i in (*.jar) do @call "%~dp0_jrubysetcp" %%i
for %%i in ("%JRUBY_HOME%\lib"*.jar) do @call "%~dp0_jrubysetcp" %%i
it works as expected...