I'm willing to put some time into trying to fix this, in the case that it is caused by my Makefile changes. However, it would be very helpful if I could login to the build-bot and try running with the Makefile change backed out. Is that possible? Having to setup a VM to match the compiler of the build-bot would take quite a bit a of extra time.
Looking at the "stdout" log file, I can't see that we are doing anything wrong. Specifically, the ".gc??" files are being removed and so I think that rules out the theory of stale profile information files messing up GCC.