I'm checking the box to Enable custom colors and the builds are not affected at all. I had this working before but now, it won't work. Weordly, the icons have the reskins and dots indicating the tiers. What could be the issue or how do I fix this?

When you say that the icons have the reskins/dots, do you mean they have the expected color, and it is only the buildings that do not?

To confirm, your custom colors that you specified in fields 0-6 are the color codes you're intending to use and not the defaults?

This is weird. When I check that box to Enable custom coloring it is unchecked when the game restarts. No matter if I select resync mods upon restart or just load. This is why the building colors are not changing. Any thoughts? Note that I took this save from a 1.0 version of Factorio and it worked fine there.

Could you send me your save?