We have encountered this problem on systems with certain ATI graphics cards. If you have to wait a long time for the pre-mission text to load (for instance "The Jim Dandy, Earth Orbit, 5:89AM" before the first orbital jump) you should try enabling Vertical Synchronization (VSync).
To do so you must enter the Catalyst Control Center by right-clicking your desktop or the ATI icon in your system tray and selecting Catalyst Control Center. If the application asks which mode you want to use, select Advanced and click Next and confirm by clicking Yes.
In the left menu expand the 3D group and select All Settings. Now, in the right menu, find "Wait for vertical refresh" and move the slider all the way to the right (Always on).
Remember to return this option to default when you finish playing MDK2.