This can get tricky and time consuming to fix. First steps are usually to isolate where the problem source is.
Can you reproduce it from the command line? Write a a script to run it repeatedly from the command line. If it does not time out from the command line then the timeout problem exists in the application that is running the plugin.
Try and get a network packet capture of a timeout, ideally from a command line invocation of the plugin. See who is not responding. If the Windows box is not responding, most likely the problem exists on the Windows side.
If the problem is pinpointed to the box running the plugin, sometimes a stack trace (strace or similar) can help find the problem.