I have this issue, too, sometimes, most usually with cams and sech that have a high multiplier. Especially if I'm using somewhat older milk. All I can do is keep stirring during ripening time (I stir up the top of the pot with the ladle @ 90 degrees to milk surface for a minute or two, THEN draw up and stir around from the bottom - it doesn't seem to work unless I do that "top o' the pot" thing). With cams, though, I almost always end up with those special little multi-colored curds - on the good side, they seem to work themselves out during the aging process, as I've yet to see the paste on a finished cam look like one of those colby/jack mixes with half-white, half-yellow curds.
Or perhaps the problem is really a secret Borg weapon and there really IS nothing we can do. (What if the hokey pokey IS what it's all about??)