i thought that was normal behavior in iOS 6.
mine has smaller icons too, although inverted. never really paid much attention to it. and i doubt cleaning the cache would help. ive cleaned caches before and as far as i know it never "fixed" it.
this is what mine looks like with standard ios 6 icons at the bottom
If you were to do as I posted above the rest of your "icons" would be themed the Elite6 style.
Oh yes duh I forgot to say respring afterwards lol. Yea I have iCleaner & it doesn't clean those either. You'll have to do the same if you choose another theme or go back to stock. But with Elite6 I think my iP5 will die with it lol.
is it safe to remove all the junk in that cache folder? including folders within?
I've never deleted anything except the mentioned above and the bsbg images. The bsbg images have to do with bitesms pop-ups. I wouldn't try anything and lose the mighty JB!