as pointed out by SourceForge user jonathan (https://sourceforge.net/p/gnuarmeclipse/support-requests/44/), there is an old CDT bug affecting dependencies creation.
in the new beta release I applied a local patch to avoid it. the patch filter the compiler command line and replaces -MT"$(@:%.o=%.d)" with -MT"$@".
the effect is that the name of targets in the dependencies files will be xxx.o instead of the wrong xxx.d.
although the bug is obvious, it is still very hard to explain how on some platforms and configurations, the dependencies were sometimes computed.
the good news is that with the patch, the dependencies seem to be ALWAYS computed.
to test this you need to have a project with header files, preferably with at least two levels of include in include. edit the inner header and start the build. if the source files where the headers are included are compiled, then it must be ok.
more testing would be highly appreciated.
please describe the procedure you used in detail, so that other try different procedures.