I'm confident you'll be able to tweak out the problems. What are you using it for exactly? Just as an effects box for your amp, as an amp simulator, or just for recording etc?
If you're just using it for effects, make sure to turn off the amp and cab sims. If you're using it as an amp sim, try plugging into your amp's slave input (if it has one) so that you're not doubling up on EQs, volumes, etc. In either case, it can make a difference what you set it up as injecting into (ie: into a combo, head, PA, etc. The manual'll tell you how to do that)
The pod's beauty and its curse is its tweakability. I got pretty good at driving mine after a little while, and I could get a ton of awesome tones out of it... but I almost felt there was too much choice, and too many parameters to tweak, so I never quite felt I was getting the best out of it that it could give...