I recently ran into an issue with Flex Builder where I was getting the "An internal build error has occurred. Please check the Error Log." error when trying to debug my project. Absolutely nothing worked including all the normal practices such as cleaning the project, recreating the workspace, manually deleting the bin folder, reinstalling Flex Builder, etc.
After performing all of these tasks I was still getting "Uncaught exception in compiler" in the error log, which by the way is the .log file in the .metadata folder of your workspace. After further analysis, I tied the issue back to a missing semi-colon after a variable declaration in my class such as:
public class SomeClass
public var blah:Object
If you ever find yourself in this situation, start rolling back code and begin to do a detailed analysis for syntax errors that normally do not pose any problems.