Mouse Freeze when Application starts

I have a recurring problem when I run an application I have recently built in Java.
During debugging, where I have been starting and stopping the app frequently, at some point the the mouse buttons become un-useable. The mouse is in this state only on the app window, working fine in other apps. I had to include an accelerated menu item to allow me to close it, as the mouse cant even be used to close the app.
I can move the mouse over the app no problem, its just the click that wont work, for example to click and change text areas, close the window, or press a button (which unfortunately are the events that drive this app).
This is not a serious problem as it only occurs after several stops and starts of the app, which won't be occuring when launched live. Despite this, I can almost always be gurenteed that it will happen eventually at some point during testing.
The only thing that solves the problem is restarting the machine. Also, I originally thought the problem came from trying to open a Socket on port 80 when another app was using that port. I then changed the piort number and it worked fine, until today when the problem started again.
Does anybody have any thoughts on this and on ways to prevent it?

I've had similar problems. However, these have occured with Java applications created by others. It's happened with the two piece of software I have which are written in Java and are from completely different developers (one is from Sun!) so I'm pretty sure it's a problem with Java itself.
The problem usually occurs for me after the app has been open for some time (how long exactly differs, but sometimes just five minutes) although once happened right from the start. I can use the mouse to switch focus to a dialog box but that's about it. As you mentioned, it's fine in other (non-Java) apps. In one of my applications, it takes every mouse movement as a selection. Given that this app is a text-editor, this is very annoying!
Restarting Windows puts everything back to normal. (For a while, at least...) However, I've got better things to be doing with my time!
Does anyone have any suggestions as to how this could be fixed? Should I upgrade / patch something?
thanks
Sam
PS I'm running Windows XP Home.

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