I assume you're using a bitmap comparison?
Not something I use myself. (WAY too prone to false failures for my liking!)
However, this:
http://support.smartbear.com/viewarticle/55590/#ColorToleranceSuggests you can alter tolerance for each part of the RGB values. This tolerance will be applied to all pixels compared during a bitmap check.
R = Red / G = Green / B = Blue. Range of each being 0-255. All colour are made up from these three. So bright red is 255,0,0 .... bright green is 0,255,0 .... bright blue is 0,0,255 .... black is 0,0,0 .... white is 255,255,255 ..... etc etc. The link suggests you can tweak tolerance on each part individually with 0 being no tolerance going all the way up to 255 being total (ie. any colour is OK) tolerance. So setting all three to a low number will allow a low variation in RGB values to get through.
Assume there are settings for this in the bitmap checkpoint when you set it up?
Sounds a bit odd to me though. I wouldn't expect RGB values to alter by small amounts on different runs unless they're something that is tweaked by the user during runtime ...