I've heard of this with other car companies. Any of you with new rims have this problem?

 

Nope. I'd expect that rims and tires are such mainstream mods that there is no problem. Now if it is something really weird like throwing on 24's and complaining the fender liners rub then I'd expect them to deny any claim. It's usually a matter of common sense.

 

I was told that wheels are fine, if you lower the car then that voids just the suspension warranty...

 

Shouldn't void warranty unless the dealer wants to make up a story.

 

They have to prove that ANY mod that you performed CAUSED the damage you are trying to have fixed. So, the only thing that you'd really have a problem with would be your shocks and brakes, if you tried to make a claim. And that is only if they are super bored and want to work really hard to deny a low cost claim.