Are you using a plate to make your halve ahead of time and storing them until its time to inject the second color? If you are do they feel oily when you put them in the mold? If oily, try washing them in alcohol and drying them well before injecting the top color. The injected plastic is hottest going to the bottom cavities first and is likely cooling enough to not be able to incorporate the oils you feel by the time the mold fills the top couple of cavities, IF you are not wiping or washing the oil off the parts made in advance. All plastics will exude an oil in storage and it can become a barrier to good welds. If you're injecting fresh plastic and this is an issue I'd try booting the heat to about 360 degrees with some stabilizer added.

I had a couple minor issues with delaminating on one bait and finally started doing the belly/bottom pours in soft plastic and then heating the medium plastic used for the injection to 360 degrees. Soft plastic will bond quicker than a medium/medium joint.