We have a class that we use all over our application, including within about 30 modules. I intentionally changed that class in a way that was likely to cause many compile time problems. I figured I'd let them error out and use that to find them.
I did a clean-build. No errors. WTF.
I went in and manually deleted the module .swf files. Clean build. Build-All. Compile time errors, yay.
I fixed them all.
Re-cleaned, re-built, no more errors. Yay
Submitted my changes to source control.
Continuous integration server tries to build (ant + build script + flex SDK), errors up the wazooo.
I look, sure enough, they're real errors. Flex builder isn't complaining. I edit the file the error is in, don't fix the error, save, and suddenly flex builder sees the problem.
I have no idea why this would happen, very annoying. If I do a clean build, I actually want to build everything from scratch. I have no idea why some modules are getting an outdated version of a class that has long since been changed.