Prompt Coming Up Repeatedly

Previously I had the problem of Prompt Coming Up Repeatedly, and turning off "Calculate All Sizes" effectively solved the problem. But all of a sudden, I'm now getting prompts for ALL my folders repeatedly, there are 20 folders that keep on popping up again and again. I just installed a software XQuartz. I'm wondering if this is causing the problem. Please help! As my computer has been taken over by this problem and I cannot even do anything because of all the prompts!
Thanks.
Thanks.