Adobe Media Encoder - compression issues (.flv) cs6 vs earlier versions

Hi all, I hope somebody can help.
This morning I encoded from a 1080p QuickTime .mov file to a 360p .FLV file.
I have previously used this work-flow with CS4 and CS5.5 and have had great results.
When I attempted the same thing this morning, for the first time with CS6 Media Encoder, the .FLVs came out glitchy in places (screen shots 1 & 2 attached).
Thinking it was a process error, I tried several different methods and all yielded the same results.
So I returned to CS4, thinking it might be a software issue, and "hey presto" no glitches!
All updates are present and correct from the Creative Cloud/ Adobe Application Manager, so am I missing something?
Has anyone else experienced anything similar? Lots more encoding to be done this afternoon and would like to use CS6 ME if at all possible.
Any help would be massively appreciated.
Darren
Message was edited by: djmulryan - amended screen shots

Hi all, I hope somebody can help.
This morning I encoded from a 1080p QuickTime .mov file to a 360p .FLV file.
I have previously used this work-flow with CS4 and CS5.5 and have had great results.
When I attempted the same thing this morning, for the first time with CS6 Media Encoder, the .FLVs came out glitchy in places (screen shots 1 & 2 attached).
Thinking it was a process error, I tried several different methods and all yielded the same results.
So I returned to CS4, thinking it might be a software issue, and "hey presto" no glitches!
All updates are present and correct from the Creative Cloud/ Adobe Application Manager, so am I missing something?
Has anyone else experienced anything similar? Lots more encoding to be done this afternoon and would like to use CS6 ME if at all possible.
Any help would be massively appreciated.
Darren
Message was edited by: djmulryan - amended screen shots

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