Actually there were two problems:
- I used some APIs from NetBeans 6.7 like FileUtil#getConfigRoot() (tagging it with since org.openide.filesystems 7.19 is not very helpfull - how can I guess when NetBeans version matches to this?)
- FileObject#getPath() returns absolute path prefixed with slash in NetBeans 6.7 but it returns relative path (without leading slash) in version 6.5. This completely broke our resolution of Android platforms. FileUtil.toFile(FileObject).getAbsolutePath() is used now to fix the problem.
My Hudson build is now updated to run tests using NetBeans 6.7 and 6.5.1 and final bits are produced as a clean build against the older one.