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:)
Examine what is said, not who speaks.
"Efficiency is intelligent laziness." -David Dunham
"When I'm working on a problem, I never think about beauty. I think only how to solve the problem. But when I have finished, if the solution is not beautiful, I know it is wrong." -Richard Buckminster Fuller
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