Don't suppose you have any sort of uneven load in the boot e.g. amps, subs etc?
It could be down to the stiffness of the lowering springs that were used perhaps you need some stiffer ones. Also were the shocks and their mounts replaced when it was lowered? If the strut mounts are knackered that could be a reason for it to sit slightly lower on one side and therefore rub.
One other thing to check.......do your wheels have the correct offset? If it is much lower than 35 they will sit out further and could cause a rubbing problem.
Toby