I have a post on my blog about this issue but i'll post it here.
This morning I ran the Flex compiler on my project and the compiler hung. I was confused as to why my project would not compile, considering the fact that exactly 3 hours ago I was running the compiler like nobody’s business, building projects left and right; I digress. So immediately, I clicked on the progress tab and a window popped up titled User operation is waiting. Well after searching Google yet again for a solution to another Flex Builder 3 issue, I had, you guessed it, no luck finding an answer.
After spending an hour or so trying to fix Flex Builder, I found out that this problem usually occurs if you have big scale projects or too many projects in general opened all at once. In addition, if you have the refresh projects automatically workbench preference turned on it will occur as well.
What I did to fix this problem is simply deselect the refresh projects automatically option in the Flex Builder preferences panel then I closed the project that I was working on and closed out Flex Builder. Once I reopened Flex Builder 3 and my project, everything worked like before. Another issue solved