If you are running your boxes through wineq2 and not say, innerspace (isboxer) or some other windowing program, you will see some errors with mq2moveutils because of the way it inputs your movement directly rather than with keypresses (or something like that)
under [Default] in your ini add the following
WinEQ=on
this tells the plugin to use the old movement routine, which while not as good as the new one, works in the 'background' when using WinEQ2 and prevents lots of wierdness from happening (like all your characters running off in 6 different directions)
Some reading also shows that changing true heading to off
TrueHeading=off
Might be of benefit depending on the nature of your problem.
I myself had to use the WinEQ=on flag for a while back in the day because I was too broke to afford innerspace.