Found it, that was a recent change where I was doing a find and replace to replace $20's to $00 (spaces for @'s for tilemaps, I must have caught that bit of code too).
Great, finally, a nasty bug tracked down and fixed! ;). Thanks a lot!
Just so you know, I also tested the text mode (HR/MC) for the Scrolling Text function. I used a "Bubble Bobble" background converted to TXT MC mode using Charpad (alphanumeric characters are included in the charset). I changed the text colors, but at this stage, the colors don't match the settings at all (see the screenshot below). I'm not using Irq or anything like that (just standard nodes).
I encourage you to run a test and see if you encounter the same issue with character color control.