I can't seem to get the color selections for the comments to turn out the way that I want them to: the coloration for the text ends up just fine, as does the avatars and author comment tracking. However, when I attempt to change the color of the background on the comments, they remain white.

This doesn't appear to affect anything else. I went so far as to delete my install of Wordpress, reinstall, manually uploaded 3.5.3, and then imported settings from a prior setup. I've tried it in both Chrome and Firefox (both latest versions) without luck. Needless to say there's no other plugins or themes that could cause conflicts, and in all other respects the theme is doing exactly what I expect it to.

I've tried resetting all theme options, then going back in and just altering the color for comments; this has no effect.

This probably is a silly question but you are trying to change the colors via ATO>Style & configure COMMENTS. Right?

Honestly at this point I've tried it via the Style & Configure Comments screen, the Forms screen, the Body screen, the Header screen, the Footer screen, and anything else I could. And as I said, I can get the 'Highlight Author Comments' colors to show up fine.

At this point the only things I cannot get to take are the colors for Regular Comment Background Color, Alternating Comment Background Color, and the grey loop around the header when I use the ata-round style (which I used as a basis for my own layout).

Duh... Stupid me... Look in ATO>Add HTML/CSS Inserts>CSS Inserts and you will see styling for comments there that are specifically for the round style. This overwrites what is in the Comments section.

Ah- that's fixed things. Thank you.