I ran into a problem with the Flex Debugger not stopping on breakpoints. Here are somethings that could be wrong:
1.) The debugger and flex may not be connecting to fix this see here:
2.) You may need to clean your build to do this go to project>clean
3.) Your browser may be caching the SWF, clear your cache in combination with the other two and see if it works then.
4.) Check your publish paths and debug url to make sure that they are going to the same place. Your "Output Folder" and your "Output URL" folder should be in the same location. You can set these by looking at your project properties and then looking at ActionScript Build Path and Run/Debug Settings>Edit
We depend on the flex debugger to do our bidding and it is a real drag when it stops working. A good indicator that the browser cache needs to be cleared or that your output URLs are not the same is that your traces are showing up in the debugger but any additional new traces added are not showing up.