I have had similar problems with chicken. There are a couple of things you can do. First, chicken is hard to smoke because the low temps make the skin rubbery. Second (and if your like me) you cant take your smoker up to 350 because I always have things like ribs and brisket on their also and that high of a temp would ruin both those. However, 350 is really where you have to cook chicken thighs with skin on to get the skin crispy. What I have done to eliminate this problem is to cook chicken thighs boneless and skinless. I have had some success in doing this and I really dont think it matters that much to have skin on or off. I trim the thighs to eveness then place a peice of rolled up bacon on the side where the bone was.kind of tuck the underside around the bacon and close with a toothpick. turn the thigh over now "skin side up" and lay a peice of fatty ham over the thigh. This will take the place of the actual skin and keep the top moist plus it adds a lot of flavor. Now you can cook the thighs at 230-250 withoiut risking the rest of your meat. Plus when they are done remove the ham and bacon and the peice will have a nice shape (kind of like a mini hot pocket) The last 45 minutes you can also remove the ham peice and start glazing.
Blue Moon Porkers
FEC100 / GMG Jim Bowie (Dealer)/ Sams Club Gasser / King Cooker Hot Tub