Not sure if this will help you -- but what I did with the stuff I have been porting over is I kept a fresh pristine copy of the packages extracted and when I ran into weird issues that make clean wouldn't fix I would just move over any source code changes into to my pristine "backup" copy. Then I would delete the working copy and then copy the backup copy back to be a new working copy. Then I would run configure, cmake or whatever needed to be ran to set it up the project again.

I found that by default I would do this when I switched between x86 to armel mode. ./configure (or cmake) would cache things for the other enviroment and so unless I reset the entire project it would have weird issues.

So my solution of a un-configured/un-cmaked/un-maked pristine source "backup" seems to work the best and be the most reliable.

The only "gotcha" is you need to make sure you copy any source code "fixes" to your pristine backup copy before you ditch your old working copy.

Nathan.