i've been doing countertop partial mash's in a 2 gallon cooler. usually mashing about 4lbs of grain. the last two recipes i've thrown the crystal grains into the mash. does this have any affect on the beer?
The crystal should be mashed with the other grains. You will get a couple of gravity points out of them, but they are still for color and flavor more than fermentables.
Temperature may play a part. Check that the crystal isn't optimal at a cooler steep temperature than mashing grain. Some crystal malt extract yield more sugar / flavour at a lower steep temp for a longer time (say over night). You may need to go to the grain manufacturer to get the answer you want.