It is likely that the files in /etc or the ones in /usr/share/texmf are symlinks to the other set of files.
That's right. Maps are kept in /etc /usr/share/texmf/fonts/map/pdftex -> /etc/texmf/map/pdftex /usr/share/texmf/fonts/map/dvips -> /etc/texmf/map/dvips
A lot of the problems you have come down to this: teTeX 3.0 is not exactly the same as teTeX 2.02 was (mostly because of changes in the TeX Directory Standard); but the linux rpm/deb packages try hard to make it appear to be. Hence the attemps to make it fit in the old directory structure (Most probably this is because maintainers tend to dislike change).
In the latest cont-lmt.zip from Pragma, as well as the latest Latin modern distribution on Ctan, absolutely everything is lowercase. The mixed case file names are a thing of the past, and indicate that not all of the old stuff is removed from your system (still).
It was a fresh install with custom font sets copied from my discontinued Miktex installation which wasn't case sensitive. What I didn't know was that I needed to regenerate stuff with texfont. In the beginning I just lowercased the ASCII files with sed and couldn't figure out where still references to the old uppercase filenames came from. BTW, I must say I kind of preferred Miktex.
Cheers, and hang on,
Taco
Thanks for the upkeep ;) But I'm still not convinced that spending half the time on the content and the other half (or more) on Context is such a good thing. -- Tobias