mp4 compression for broadcast

Hello. I have a quick question about mp4 compression for broadcast. I am a video editor for a local news station, and we are migrating from beta to a tapeless workflow. We are currently shooting on the Sony EX3, and editing in FCP 6.
We are dabbling in FTPing some of our video from the field, but are having some trouble getting the correct compression settings. Photogs in the field are using the EX3's, cutting in FCP 6 with the Aja Kona 1080i 29.97 8 bit uncompressed setting. They are then exporting using QT conversion, mp4, and then ftping the file to our server. However, many times the file looks stilted or pixelated when we bring it into our edit systems back at the station. One other thing I should note is that we currently bring in those mp4's into an SD editing setup (aja kona 525 29.97 8 bit uncompressed, as we still crash to beta). I am thinking that it is a frame size setting that the original sequence is being exported as that is causing the problem, but was wondering if anyone had any thoughts or advice .
I realize this is a lot to digest, and also that there are probably better ways of doing this, but let's just say that 9 months ago 90% of what we were doing was tape to tape..... Thanks for any help.