I have installed FMS version 2 beta 7 on two separate Win2K machines, now, and have observed the same behavior on both. I am using the keyboard controls. To accelerate, I hold down the G key - but it takes a LONG time for the throttle to kick up - and it kicks up a notch in approximately 1-second intervals. The animation is the same way - advancing a frame every second or so.
On one computer, it is set up to dual-boot Windows98 & Windows 2000. If I boot in Win98 and run [an older version of FMS], it runs just fine. I haven't installed the latest version under that operating system, but the same computer running the latest version under Win2K stutters.