Your best bet is to go to a reputable car audio store in your area, preferably one who sells high end stuff, and can diagnose your problem more readily. I had the same problem, and replaced my antenna as well as head unit, and now everything works awesome. BTW, I have never had a factory head unit in my truck. Drove it off the lot, and had a Kenwood Excelon unit in it 2 hours later. I have sinced put an Alpine unit in, and think this is the best head unit ever... If I were you, I would get a new head unit as well as new antenna, and you should be good to go. Good luck on whatever you end up doing, and keep us updated!
-Chris-