Desktop AIR app debug build running from cache?

I'm new to flash builder (using 4.5 for os x) and I've been working on a desktop AIR app for the last week. I've been running into a strange issue when deugging my app. Every once and a while (maybe 4-5 times a day) after I make changes to my code and I make a new debug build, a much older version of the app runs when I run the app with or without the debugger, or even if I export for release. It's as though its running (or building) from the cache, except I'm building a desktop app and I'm not testing the swf on a browser. I've turned off "Build Automatically", cleaned the project and build again but no changes are reflected. I can't figure out how, but after cleaning, quitting flash builder, restarting, cleaning, building again, etc.. numerous times suddenly I will see the current version of the app back up and running. I cannot for the life of me figure out how to quickly resolve the issue, or what exactly is fixing it. Every time it seems like something else triggers FB to refresh the build. I can even run the debugger and step through my current code while seeing completely different results on the screen.
Has anyone else run into this issue? Anyone know what I may be missing? Are there settings I need to change besides "Build Automatically"? Thanks for your help,
Nick

Thanks for the answer. How exactly Flash Builder is running is a little clearer to me now. I checked and the timestamps were indeed being updated correctly.
This helped me to look elsewhere for the issue. I actually now think it may have to do with mobile home sync that I have going through OS X. Whenever the sync runs, FB seems to launch an outdated (as in hours ago) version of the app. Despite the fact that the sync is not pulling in new files, it seems to be the issue. If i stop the sync I start seeing the current version of the app again when I run the debugger. So I think its just the OS causing my problem (although I still don't completely understand why exactly the issue would manifest itself in FB). Fortunately I can recreate the issue every time I run the sync, so the problem is consistent at least!
Thanks again for your help.

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