Internal build errors are the bane of my existence, and they oftenhave nothing to do with my code. I posted a large number of solutions and causes I'd found on my old blog, here, but sometimes they still happen and for no good reason.
From what I've seen, Flex Builder seems to crap out and stop compiling if there's more than a few hundred classes in your workspace. The best and most consistent solution I've found is to clean and rebuild until the error goes away.
Why can't Flex Builder do this for us, or at least try it a few times before throwing the error? The answer is: it could, but it doesn't, and all it takes is enough people asking Adobe to add this feature for it to become a reality.
Please join me in the fight against internal build errors by voting for this enhancement request.