Java reflection property works in Linux but not Windows

I'm working on some code that is acting strange. The code is using the Java reflection property, loading the method name from a JSON file. Works perfectly in Linux, yet, importing and running the same code in the same IDE, with the code running in the same version and profile of a Websphere Application server setup, they are both using the same source files through a file server mount. Other parts of the application manipulate these files without a problem in both environments. Yet, somehow in Windows, it is unable to load the method from the file while Linux can. Stepping through the debugger in Windows I find that the null pointer error occurs at the time of trying to dynamically load the method, while stepping through the code in Linux in the same manner it simply proceeds where Windows gets stuck without issues. I'm getting this null pointer error from the application pointing to a method that does not exist due to the failure to load:

java.lang.NullPointerException
at com.mpi.factory.ToolStateFactory.getToolStateExtended(ToolStateFactory.java:19)
at com.mpi.factory.ToolStateFactory.getToolStateExtended(ToolStateFactory.java:33)
at com.mpi.factory.ToolStateFactory.getToolStateExtended(ToolStateFactory.java:41)

Given that the JRE is supposed to be portable and it shouldn't matter in what environment it runs, I suspect it's related to the OS. Has anyone experienced this issue before? I'm wondering if it's something that needs to be addressed at the OS level, or Java security settings? I know Windows is a bit more glitchy when it comes to drive mounts than Linux. I'm wondering if it's an obvious, well known issue with J2EE projects trying to use reflection in Java. I really don't think this has to do with the Webpshere, or project settings (Classpath, Deployment Descriptor, etc) since they are identical in both environments. Can't really find anything online about this quirk.