Many universal remote controls are compatible with the ReplayTV. I have one of the oneforall models with a PVR device key and it works well. The down side is that it doesn't have the Zones button. For normal viewing, this is a minor inconvenience. You can access Zones through the menu using two or more button pushes instead of just one. However, the Zones button is needed for some of the special functions. An example is 243 Zones to get to a menu which provides a forced network connect. I keep my original remote control, which has a number of buttons that don't work well, just for the Zones button.
I agree with dstoffa and gring40 that the remote is probably not causing your machine to crash.