I noticed the same thing. I'm trying to get to Greece and would prefer to fly through FRA, or any European city from IAH. Unfortunately, they are trying to get me to fly to ORD, DUL or EWR first. I noticed that even though the direct planes seem pretty open (I checked seats), they were not offering the mileage options nor the lower fares. I could only find the flights by putting in First Class vs Economy.

I'm guessing it is because they have JUST completed the merger and are still working through the flights. I'm giving it another week and then going to call the 1K desk for help.