David,
It is really odd, but I seem to be able to reproduce this.
I will have to do some additional tests to see if it is my perception or a problem with either gmake or Eclipse, but I see my pre-build step running and I also see gmake calling the four processes (-j 4), therefore it is unclear where the issue is coming from. If it is from Eclipse we may be able to fix, but if it is from gmake I am not so sure.
I'll get back to this thread after checking some additional things.
Regards,
Rafael
P.S. Eclipse CDT has a related bug filed that references the same options, therefore I wonder if it is influencing this behavior.