Severe anti-aliasing when exporting via compressor

Hello all, can't seem to find anything to answer this in a search, so any help would be much appreciated.
I seem to be getting severe anti-aliasing whenever I export anything from FCP to compressor. At first I thought the problem was with compressor, because everything looks and exports directly from FCP perfectly. But if I open compressor and import/open the exact same movie directly, compressor seems to do its job as expected, so I'm pretty sure I've narrowed it down to when I export something 'using compressor'
I've tried various different codecs and sequence settings including totally 100% uncompressed, I've also tried upping the bit rate and everything still comes out looking exactly the same.
I have a feeling I've accidentally changed some setting(s) somewhere (although I can't think where or how) because until a few weeks ago, everything worked just fine.
I think I'm going to have to re-install everything, which I'd obviously like to avoid, so if anyone has any advice or suggestions I'd be very grateful.
Thanks in advance.

The anti-aliasing preference setting in both Illustrator and Acrobat is just a preview on screen.
If you're going to print it preserving the jagged nature you could apply Effect > Rasterize with appropriate settings in Illustrator, for example.

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