Try using a softer plastic in the belly section. The softer plastic welds better at lower temps. Maybe try adding some stabilizer to the top color, more than you think is necessary, and jack the shooting temp up to 355-360.
As Andy has alluded to, don't shot the bellies one day and then add the top color a week down the road. I shoot 3000 chartreuse and hot pink tails for a couple of paddletail baits I make and have had nothing but headaches with weld separations since. The only way I can use these now is to count out how many I plan to use and give them an hour long bath in alcohol to get rid of the oil that naturally exudes from the plastic. I now shoot [pour] the bellies and re-shoot in that order, every mold, and I have no issues with color separation.
If I am doing a simple two-color bait but in larger numbers, like 100 of that one color combo, I'll do all of the bellies and then immediately go right back and lay the top color on, but I add stabilizer and extra heat to that top color and add some softener to the bottom color.
Also as Andy has alluded to, if you are shooting the top color in and having it run under the belly section as well as atop of it, you are shooting too hard/fast. Something to keep in mind though is that when a belly is hand poured into the cavity, surface tension makes it stay in place like its glued there. If you remove that piece, the surface tension gets broke and that will make it much easier to have a top color get under it when that injection gets made....just something to think about.
