I started gpsapp and it got a fix. I started the car, and gpsapp was gone from the hijack menu.

Yeah, that could very well be a hijack bug, I noticed it myself. The menu entry is only shown when the application is blocking in WAITMENU.
Sometimes, like when the car is started, hijack seems to 'forget' that there was a overlay active. The display and button redirections are removed, so the player becomes visible again, but the application is still in it's main loop polling for keypresses which ofcourse never arrive.

The little pointer in the map area should always be 'true north' up, the other pointer points to the direction of the next waypoint, but is relative to the current direction. So if it points up, you should be driving straight to the next waypoint, and it points down when driving away from it.