thank you very much, that was exactly what went wrong.
Just for Info: we had the profile "main". main runs well on Samsung Galaxy Tab GT-P1000 and on the 7.7. but the size on the 10.1 for this profile seems to be restricted to max. 720x480 px
Videos with "baseline" run well on Android Devices and on the iPad as well.
alright, I tried like 100 different things and here's something that works.
I put my video in After Effects (so I guess you can do the same with media encoder, but at least here I'm SURE it works fine)
Put your video in a 1280*720 comp
resize it as you want inside the comp
then render with these settings (ok it's in French but just transpose in the boxes)