Almost anyone who owns an early version of the NexStar GPS has watched their scope loop all the way over while finding level and wondered just how dumb a computer can be! While generally amusing, it can be horrifying if you happen to have any accessories that are damaged by the unusual positions of the optical tube assembly (OTA) during these maneuvers. It is easy to prevent. Before starting the alignment, insure the OTA is pointed 10-20 degrees below level. The level position is located only as the front of the OTA is moving up.
Please note that this is no longer required with hand control version 1.6 or newer. The new hand control dips slightly at the beginning of the GPS alignment routine, so starting with the OTA approximately level will be sufficient.