I'm not sure this is what you are seeing (since you say CPU usage is ok - is this the total on all cores, or are all cores ok if oyu look at them individually?), for me this happens when I the CPU core which most of MegaGlest runs on is entirely maxed out. In this case the total CPU load is still mediocre, it's just that the main thread is completely busy, so the processing stops repeatedly for short sequences.
Which faction were you using, what was your game setup? Does this always happen, also on 64x64 maps with just two players playing the same faction?
Is this MegaGlest 3.7.1 on Windows 7?