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 I have no idea why some modules are getting an outdated version of a class that has long since been changed.

I experienced that too..
Did you by any point rename your modules ?
try to make a new moduel, and copy the code from the old module. It works for me.
Rasmus
Unfortunately renaming the modules is not an option. This project is just too big with too many modules and a large enough team working on it to make that easy.
I’ve had this issue as well… many times. I’m very curious to see if there is a fix out there!
Hi
What do you mean with too big?
I’m asking this because i’m planning to move a portal made in .net to flex so i’m searching information about how to work with modules and i can’t seem to find real working examples, i only find those simple examples from Adobe. Can you help me on this?
I mean that renaming the modules can cause these problems, in my experience..
My solution was to make a new module, from scratch, and then fill in all the logic from the module that wont compile.
@Elias – I meant the project is really too big for me to realistically refactor the names of all the modules. Something that Rasmus might not have meant me to do in the first place, so maybe the point is moot. In general, modules work great with little effort. You can take those very simple examples in the documentation, add tons of complexity, and it still generally works well.
@Rasmus – I hadn’t renamed any of the modules, and I understand what you meant now.
As for the solution, it was a couple-fold,
1) I used the unix command touch to update the timestamp on all of the flex module files. This seemed to make some of them rebuild.
2) I used the output from the ant build script to find the errors and fix them, once the actual file was modified, that module would successfully rebuild in ant and flex builder.
When I have similar issues, I check the build order of the projects in Eclipse and refresh the source paths (files in source paths are not always in sync with the files in the original project). After that, cleaning all projects has worked out fine for me (within the limit of all FlexBuilder bugs…)