I've had some email correspondence with Jeppesen WRT the route issues, and NDBs being used instead of VORs. Their last response to me on the issue, was:
(my bolding)
30 August 2011
Good afternoon Capt Claret,
Your service request has been escalated to my attention. I understand that you’ve been having some problems with various routes not being accepted in the Mobile FliteDeck application. It appears that most of the routes in your example include a VOR entry/exit point that shares the same ID as a nearby NDB (e.g. GV, CS, AS, AYE). This is causing the problem, because the application will sometimes default to the NDB if it is nearer to the direct route. However, since the NDB is not the entry/exit point to the airway, the route fails. This is a known issue that our Development group is aware of and are working to address in a future update to the application. I apologize for any inconvenience this may be causing.
Best Regards,
Xxxxx Yyyyy
Tier 2 Technical Support Specialist - Nav
Technical Support Services
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Jeppesen
A Boeing Company