try compiling with -va
This will cause a flood of information (many 1000 of lines, so make sure you capture the output in a file)
It will tell you for every file, all the paths that have been trie, and what was found (or not).
First look (grep) for any other fpc.cfg file.
Maybe in your users home dir, maybe elsewhere (/etc/fpc/cfg is not the only location).
If no unexpected file was found, then check where it did look for the system.ppu, and where it found it.