I'm seeing an issue in debugging a Flex 4 project in Flash Builder 4, on Mac OS 10.6: when I double-click the grey bar to the left of the line numbers in the code editor, which is normally how I set and remove breakpoints, it appears to have no effect (i.e., existing breakpoints aren't removed and new breakpoints aren't added.) However, in the Breakpoints view itself, the breakpoints do show up correctly in response to double-clicks. It looks like there's a synchronization bug between the actual breakpoints, which show up in the Breakpoints view and do actually work, and what's shown in the clickable grey area. This bug appears and disappears sporadically; I haven't figured out a correlation with anything else I'm doing. Pretty annoying when you're trying to debug.
It would be great if you can provide us with your log file.
It is at workspacedir/.metadata/.log