Sounds like faulty files. Reinstalling and/or manually deleting the files from your folder (that is, the mod folders, not ETMain and the overlaying folder) (being the pk3 files, maps and mod adjustments) should always fix this.
I've had a similar problem that would occur if my folder was simply too sizeable.
The problem that you are having does not sound like one that you can fix in-game. com_maxfps 125 is nice if it has been limited before, but I believe it is set to well above 125 on default. There is, as far as I know, no server option available to forcefully limit its clients FPS with the com_maxfps command (as it is client-based(?))
/e As I read on it seems that a lot of people suggest making backups. Just like virusscanning; the more you leave out of the scan (or reinstall, in this case) the higher the risk the problem is contained within a file that is not checked.
Edited by Flible, 29 April 2016 - 11:28 AM.