I’d like to return to this topic, if I may.
This issue seems to persist, showing up on multiple operating systems (Ubuntu, Windows 7 and Windows XP) and at least two computers.
I really am mystified: the prc file does seem to be found and at least partially respected, because at least some options seem to work, but not all do.
Another thread mentioning a similar issue was posted more recently; I decided to bump this thread rather than that as that thread had other potential muddying factors (such as uncertainty regarding the presence of the “p3d_info” file, which I think that I have observed in my p3d files).