dgwyn,
I'll take a stab at your questions...
"I lost my alignment three times over a three hour period": sounds like the scope/software is locking up. Since it happened with PemPro, then AutoStar's remote handbox, then after a GPS fix, I would suspect the connection between the scope & computer. Assuming that you are using a USB to R232 adapter, it is most likely the cable. Several brands (including Belkin) are known to cause problems. Power supply problems can also cause these type of "lockups"
Again, this is just a guess. More detailed information is required to narrow the issue (AutoStar version, power supply, etc.). And a smarter group of people to help you, than me.

If you can't find an answer here, the next best resource (maybe even better) is the LX200 GPS Yahoo group. The world's best experts hang out there (Dr. Clay, John Mahony, Dick Seymour, Andrew Johansen, etc.). If the problem can be diagnosed & fixed without sending the scope back (likely in your case), these guys will know.
Jim