Extra Thread in Debugging with eclipse

I am having this issue, that really bugs me and everyone else arround as well.
One of our service classes extends Thread class and servers simply to display a little animation window to show that application is processing.
It's run method looks this way

while (true)

catch (InterruptedException ie)

I am not even looking at this class, because debugging something different. However, while in debug mode in eclipse, the debugger behaves in such a way as if I had a break point in the run method provided here and the break point is on in the first wait() method. I have to manualy hit resume for the debugger to keep going. That was annoying but but manageable, but now, if it happens the whole application freeses and I have to restart .. this making the debugging impossible.
Has anyone seen this issue? I think it's a JVM or something. Can someone point in the right dirrection
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