As Heda has pointed out in this thread in the Reaper Bug Reports forum (http://forum.cockos.com/showthread.php?t=134677
) this bug only occurs in the Arrange view and NOT the MIDI Editor. The MIDI Editor seems to work perfectly from tests I have done.
With this being the case, I can only assume Justin/Schwa already have the programming logic to get this fixed and the same logic just needs to be applied in the arrange view. Maybe the code for the Arrange view is different and more complex which would explain why it has been nearly 2.5 years without a fix? (from when Heda first reported it).
I know it might not be as important as some other bugs causing crashes etc, but I would still really appreciate a fix for this as it really detracts from the look and feel of Reaper for anyone using colored regions. Even if a method fixing this was made available through the Reaper API that would also be sufficient for me.