Filux was hosting today, with a newer version of the Prax mod. After modifying it he increased the mods' version number, so that it is actually handled like a new mod.
So he was hosting on Linux with this "new mod" and Atze and I (both Linux) connected to him and downloaded it. Both Atze and I got a "techtree different" warning for the techtrees' single "Natulka" faction right after downloading. Then Atze and I disconnected and reconnected, but the warning remained.
Then Atze and I restarted our clients and reconnected, but the warning remained.
Then Filux restarted the server and Atze and I reconnected, but the warning remained. Interestingly this time, and before the Prax warning, I also got a warning about differences in the Aqua Pack techtree (probably the first in the list) which was not currently set (see screenshot). Also both warnings are about the Natulka faction which is not present in Aqua Pack.
Then all of us cleared ~/.megaglest/cache/ and restarted server and clients and reconnected, and only then the warning was gone.
So there still seems to be a difficult to find bug there somewhere.
Screenshot of when Atze and I reconnected after Filux restarted the server (cache yet untouched):
