We use Concur as well. I've often seen a discrepancy between the Concur reservation and what appears on AA.com. Many times my seat selections in Concur don't "stick". (Particularly if I'm selecting MCE.) The first thing I do after getting the ticketing confirmation from Concur is login to my account on AA.com and select my seats and request 500 mile upgrades. (Or if I find availability through ExperFlyer, call to upgrade with miles and copay.) Sometimes it takes a while for the seat changes to reflect on Concur, and therefore on TripIt Pro.

Since we have strict policies in place on ticket prices and class of service, I can only book Economy class, then upgrade on my own. On an upcoming trip to Toronto, I found the difference in Economy and Business to be reasonable, so I called to pay the difference and purchase the Business seats. No problem, except they charged $50 for the service (increased from $25 just a few weeks ago according to the agent) because my original ticket was purchased through a travel agent. I was told the only way to do it for free was to go back to Concur/AmEx to make the change. Not worth the hassle, and I figured the fare would be gone by the time I connected to our travel department.

Note that I've never been charged the fee for upgrading with miles and copay.