It may be from undoing your brush strokes, which is telling the program to go back to the last step (which may have been locking one of those layers). In any case, you should get a pop-up message asking if you want to unlock the active layer if that's the issue.
Can you post the exact steps causing it to happen? Also curious what version of Flash you're having issues with.
Hmm interesting theory...I do press undo a lot, but only because I'm trying to get a good-looking brushstroke down, usually I don't even actively lock a layer as a step during my session because they've already been locked previously and I don't need to lock/unlock them often. The thing that is frustrating is that I will try to make a stroke, and can't because the symbol pops up...then I'll make the exact same intended stroke again and then it will work fine. It's pretty haphazard but basically every other stroke or every few strokes, it'll pop up.
I think I'm beginning to almost accept this rhythm in my workflow
I'm using CS6, and I noticed that I don't have this problem when I bring the file to work on at my job (CS5) or at school (CC).
Edit: I tried to test your theory by drawing as much as I could without pressing undo...I was pleasantly surprised to not run into any issues with the paintbrush, but sure enough, as soon as I switched from the paint brush to the eraser, and tried to erase something I just drew, the eraser popped up with the "prohibited" symbol.
I just realized my issue!
Sorry, it is caused partially from my impatience; I get the "prohibited sign" when I press a hot key to switch from one tool to another and try to make a stroke when the tool hasn't finished "switching." So I'll press my "e" hot key intending to switch to the eraser tool and I'll immediately draw a stroke, but I recently noticed that the toolbar had not switched from paintbrush to eraser yet by the time I was drawing.
So, I'll either check why my computer's so slow, or I'll try to be a little more patient, or both
Thank you for your time!