Slightly cooler plastic will probably give you better twin injections if you're doing the 90 degree thing. By the way, you can get some pretty nice baits doing the 90 degree injections but straight in injections will give the best color separation. Straight lines will have to be done with a plate. Personally I like two color baits with some blending at the color merger....they look far more natural.
That ball chamber would bother me if it were my mold, but I'm about ready to spring on a mold that it cut just like that one you have. A friend and I want a certain bait and can get the mold but it too has that round cut-out ahead of the bait and after the runner. We want this mold for two color baits, but we're looking at tail color, not a split color so that chamber should not matter. But I'd bet a buck that the plastics are swirling in that round spot and is why you're getting fudged bait coloring.