Are you sure you used the Awards & Upgrades tool and not the Flight Availability tool on EF? This is the only way you will see C inventory. Also, EF has direct access to AA's inventory and my experience with all classes of awards and upgrades has always been spot on between EF and AA.

Another possibility, although remote, is that you are getting AA's so-called expanded inventory which they sometimes make available to EXPs. EF does not have access to this expanded inventory if it is available for a particular flight.

I suggest you email them with the specifics of routes, flights and dates if you think this is an ongoing problem.