I don't pour in POP molds, but have dabbled in pouring different color tails in my silicone molds, and it definitely helps when the mold is warmed up to temperature. The second color needs to be poured as soon as you can while the first color is still liquid is just starting to solidify. A cold mold will cure that first color faster, so there is the issue.
What I have been doing is pouring my one color baits first, then do the two color baits last after the mold is quite warm. If all I am going to do is the two color, I'll heat up some garbage plastic and pour 10 or 12 baits just to warm the mold some.