If i understand you right, you have 2 cues with the same color for your moving head, but when you switch from one cue to an other the color wheel does a "rainbow" effect.
This is probable because the cue with the "rainbow" effect do no get the exact same DMX value than the previous one.
What you can do is to load the cue doing the " rainbow" effect, by clicking load in the "edit" window and then click on the cue. This will load the values stored in the cue inside the programmer.
Now you can see if the color wheel is still rotating or not. If yes try to slightly decrease the value of the color fader, this should go to the right color without activating the "rainbow".
Once done record this new content on the same cue.
I hope this will help you,