My hat goes off to you, sir, for making 5.5 your working version in its present form!
Like you, I find those little square color buttons unintuitive, not to mention buggy, which doesn't improve their acceptance. The color swatches we had in 5.0 were trouble-free. Unlike you, I found that although they went away after I Canceled them, they didn't stay away, unfortunately. So there seems no way to get rid of them once you've chosen a non-standard color, or am I wrong? Maybe we need an Option not to display them at all! I also think that when they appear in Preferences > Colors their effect is to obscure the display, making me wish they didn't. The only reason to make me continue using their new color selector for Thought types is the fact that they've linked the Plex to it so that changes to type colors are instantly visible in the Plex. Thank goodness for that. I'd say, forget about those little color squares and simply adjust colors using sliders and numbers.
PB 22.214.171.124 on Windows XP, J-1.6.0_17