Is your booster a "1 in, 3 out" type? Are you using a proper roof antenna, or an indoor one?
Remember you can have the best signal strength in the world, but it doesn't matter if the signal quality is rubbish. Maybe try adjusting the gain on the booster (start low/off, and try increasing it in small increments, see if it makes any difference).
In the name of diagnosing the problem (I am not suggesting this as a permanent solution), maybe get an indoor aerial (assuming you are using a roof one) and hook it up to one of the tuners. Tune the channels and make sure it works OK. Hook up the roof antenna to another tuner (I would suggest leaving the third one out of it for now). Then try it out. If it works, they you'll know it's a booster/antenna-related problem.