Without sight of your code your question is a tall order, but chances are even if you posted some minimal code I wouldn't have the requisite to run it.

So, generic advice, don't try and access/maintain your gui from anywhere except the main thread. When you have a "long running operation", use a thread to do the processing, but don't try and display the results directly, but instead post a message with information required to display the results to keyboard/mouse input processing queue. Have code in your main thread to look for and process the message posted, and update the display accordingly.

Sketchy answer, but so was the question:)