This is what MotionX replied with:
"Thanks for contacting the MotionX team. MotionX-GPS Drive is passive during the signal acquisition and reception. The iPhone's iOS handles all of it. We receive the exact same GPS reception/signal that is used by the iPhone's native map client. If MotionX-GPS Drive is unable to receive a GPS signal, it's because your iPhone isn't providing MotionX-GPS with location data. It may appear as if other programs are receiving a GPS signal, but they may be locating your position using cell tower triangulation instead. For example, the native Google Maps application will show a static blue dot to identify your location using network triangulation even when GPS is not available.
We have seen that problems can arise if a cell tower is incorrectly mapped by your service provider, this issue is more pervasive with Verizon iPhone users. 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.
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."