Do you understand how vectors are rasterized for pixel-based codecs in After Effects?
Do you understand the various ways in which highly compressed codecs like H.264 and WMV differ in how they quantize between keyframes?
Do not export from AE even though you can. Instead, render out a lossless movie and then use an encoder to to produce your transcodes and compression.
Yes, I think so to the first one.
No to the second. Please could you explain if its not too much trouble?
How do I render out a lossless movie?
Like I mentioned above, H.264 actually works fine.
Thank you and sorry for my ignorance. I'm still getting to grips with the software.
As Bogiesan tried to hint at - it's simply the compression and short of increasing data rates until they reach the ceiling, there is little you can do. Adding some grain might improve the compression pattern visually (though it makes the compression worese in a technical sense), but that's as good as it gets.