I run Megaglest in a separate X instance. Sometimes (almost always), when I pause the game, switch to main X server (Ctrl + Alt + F7), do whatever I want to do, switch back to megaglest and unpause the game, the game start running very fast, as in fast forward. Pausing the game for a while and then unpausing seems to fix the issue.
I am running Arch linux, 32bit, with Megaglest 3.5.2, I had same issue with 3.5.1. Didn't try running game in separate server before that, so can't say anything about previous versions.
Not sure what other info would be useful in this situation, let me know if you need some more info. Here's the script I use to run the game, just in case:
#!/bin/bash
DISPLAY=:1.0
xinit /usr/bin/megaglest $* -- :1