Red frames popping up after upgrade to media encoder cc

I'm having some issues with Media Encoder CC. My workflow is AMA SxS card (footage is in XDCAM HD 1080/50i) into Avid Media Composer 6, edit, and export as XDCAM HD 1080/50i mxf file into a watch folder that Media Encoder picks up and converts to SD mpeg2 (its the way the TV stations want it) that file is then ftp'd using Media Encoder. It used to work fine with Media Encoder CS6, but since I upgraded it keeps giving me red frames (cant read frame errors) usually just before or after there is a cut in the footage. I've resorted to transcoding the footage in Avid to DNxHD 120 after editing and that seems to resolve the issue, but it's just an extra step that adds loads of time to my workflow.
Avid Media Composer 6
Adobe CC
HP EliteBook 8760w
Windows 7 64bit

The whole point is that I dont want to transcode into DNxHD at all, DNxHD is the extra step. The can't read frame errors are also very inconsistent in Media Encoder CC.  I might export a file and it gives me a few red frames (can't read frame errors) but if I then take the same file and rename it they sometimes work.  I've tried uninstalling and reinstalling but that hasnt helped...

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