Matte made with rotobrush is different in output than it is in After Effects? Help Please.

I ran into this issue last night when I made a matte with a rotobrush. Everything looks perfect when I scrub through and even go frame by frame, but when I export it I get this issue where there seems to be "extra" matte that is cutting off something in the scene by putting the background on top of it (this is what the intentional matte is supposed to do, but not in the frames where it keeps showing up).
I'm using AE CS6 (trial version) with the latest updates. The source footage is h264 (originally AVCHD intelaced, deinterlaced using premiere pro before importing into after effects). The output is h264. Has anyone seen this before? and can you offer any advice on what to check?
Other possibly important info is that there are 3 different rotobrush mattes on 3 different layers. One covers everything, another covers things half way "through" the scene (3D), but gets covered by closer things, and the last one is for when the camera gets to the other side of the subjects.
So far I've checked:
-The matte itself.
-Made sure I drew the matte with the rotobrush at full res.
Any quick help would be greatly appreciated because the deadline for the video I'm working on is tonight. (Sept 12th).

some thoughts/questions
I would...
use the original footage, no need to deinterlace first, interpret footage correctly, precomp if required. maybe at twice frame rate to compensate for the inter field movement...
though I agree transcoding to pro res makes it easier, the right set up can cope with native footage.
I would put a bright colour solid guide layer underneath to check where holes in the matte could be being disguised by the background colour.
Check for after effects nightmare premultiplication of layers and maybe change layer mode to alpha add in case overlapping edges are causing unwanted transparency.
always render out to an RGB codec as AE is rgb based, then compress in AME...
ALways work at full res, full size.
MANUALLY delete the cache folders as you can quite often be looking at old and corrupt caches.
I have ioFX cards which really help the smoothness of roto...

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