cgroth, something worth trying is to follow these steps, as it worked for me with a similar problem with an mx-3000 using rf.

1) Uninstall your3000 editor
2) Download a new copy from urc's website
3)load a blank configuration into the 3000, then follow it with your programmed file.

This will ensure you are running your configuration with the most up to date version of the firmware in your remote.
Also, is your mrf-250 pluggged into a surge suppressor?