[Anton Nordstrand] “1080×1080, 2 pass vbr 45-50”
here is (at least one of) your problems.
You render to a delivery codec, probably H264, we can’t know in probably 420, again, we can’t know.
So, you loose half your color resolution and get compression artefacts.
Now I don’t know the encoding software, but perhaps there is kicking in a scaler as well (that should not do that, just a crop.)
But, before posting here, did you spent an hour or so testing other encoders / codecs / settings like the rest of us does here to learn how it works and be able to answer questions like this?
Bouke
http://www.videotoolshed.com