I recently upgraded to TortoiseHg 2.1.2. I used branch coloring extensively, with this line in my hgrc:
branchcolors = release:#FF0000 test:#00FF00 development:#0000FF
That is, release was red, test was green, and development was blue. Now when I load it, release is blue, development is green, and test is red. Trying to change the colors hasn't helped. It seems like it's randomly assigning those 3 colors to those branches.