In this letter MotionX acknowledges that cellular or wifi location data can disrupt the GPS signal. However, this still doesn't explain why it loses reception after it has a lock.
Chris,
Thanks for your patience as I know this issue can be very frustrating. After further investigation of your concern I have some helpful information with may shed some light on the situation.
Problems can arise if a cell tower is incorrectly mapped by your service provider. Let's say they incorrectly map a cell tower that's in Oregon to be in Texas. Now everyone is Oregon who's trying to acquire a GPS signal is either shown they are in Texas (based on the tower identifier) or they are unable to acquire a GPS signal because the iPhone is listening for the wrong satellites. This particular situation has happened and you can read about it here:
http://arcelay.vox.com/library/post/fix-for-iphone-3g-gps-problems-turn-of-3g.html
The short term fix was for users to turn off their 3G service. Then the GPS signal was acquired quickly. The same problem can arise if a WiFi access point is incorrectly mapped to the wrong location in Skyhook's database. If their database shows the access point is in Santa Cruz, but someone moves and takes the access point to Utah, they may have trouble acquiring a GPS signal while in proximity to the access point until the location is updated in Skyhook's database.
As for why the native maps app works, I can only speculate Apple doesn't show when a signal is lost immediately in the map app as we do.
I hope this information helped. Please contact me if I can assist you with anything else.