I have seen something similar on every computer I have tried Mach2 and 3 on.
All of them will run close to the selected kernal speed, but every once in a while the freq will drop by about 70-200htz (by, not to!) for a second or two. 45k was worse than 25k kernals, but all kernal speeds did it.. When this happens the mill stumbles but usually is able to keep going (except for when running in 45k kernal, in which case the mill usually stumbled and then error out). The computers have been a laptop P3m 1ghz, a desktop AMD XP3000+, and a desktop Intel P3 2.4ghz.
The faster the machine, the less the freq dropped.. but they all did it. One was a clean install, the others were from various walks of life but strong running computers.
I fixed the problem tho. G100. Never a glitch since!