Thank you Taratoga for the solution! The models are now rotated right. However, there's still some issues with some of my models. When hitting the animate button the models scale down and change their relative posiotion to the MED origin point (also, the models have some offset to their bones, but that is easily fixed in MED).

These issues don't occur with simple testing models, but they do with complex models with bones derived from CS Biped. So, I'll have to check whether this is a MED related issue at all. If someone has experience with issues described above, please share your thoughts.

As for changing the pivot point of a model. When trying to fix the rotation problem, I noticed that rotating the pivot point of an object in 3ds Max didn't change anything in MED, but rotating the object in sub-object mode (for instance, selecting all the vertices of a model and rotating) did. I guess it could work also for moving relative to the pivot point.