On iMac mid 2011.
I have a short duration (2min) sequence setup for preview files as ProRes HQ, 1280×720, 25p. The clips are all MXF from a Canon XF300. Some of the clips are green screen over a Premiere generated color matte.
When I export this sequence directly from the export window or by queuing to AME I see no problems exporting to any flavour of ProRes.
I went back and inserted some new Premiere generated color mattes and also had no problems during export.
Is there anything I can check for you?