Are you using Shrink or Springtomize2 to make the icons or fonts bigger (or both)? Cause after a certain point, they get too big and everything is a mess.
There is only so much space allotted to the icons and the labels. You can make them bigger, yes, but once they've gotten bigger than the space Apple has designed for them, they will overlap.
That's all I can think of as to what might be happening. Hope this helps.
Marilyn