On the Acquisition forums, something like this is called the lost downloads bug and it's been occuring for a long time there. Have you ever installed Acquisition?
I'd thought it was a Cocoa bug since it rarely shows up with LimeWire , but maybe you've reproduced the conditions to show it has something to do with the way Java works on OSX.

Any chance you can reproduce it and keep the Console logs? Lots of users wold be really glad if it turns out you can find something useful about what makes this bug stink.

Sorry I can't help more--much more info is needed to find the conditions that make it happen.