Well the problem isn't Milkshapes end it is more likely DBpros - reason anyone?
Well i'm gonna guess no one is actually aware for the setups and updates - however the MD2 format importer within dbpro has no doubt been developed to the exact specs of the MD2 format - this means 512 frame of animation, however this was altered when the Quake2 engine full source was released ... and now allows upto 4096 frames of animation.
This could be problem one, there are many other value updates that are probably just too large for an exact spec situtation. Read the readme on Milkshape's updates (as the plugin is mostly metes own handywork)
i'm kinda compiling a lil report right now on the formats and (possible) problems - should be reading in a few days.
[b] New interactive driving system... i like my new blue and black steering wheel

[b]