Solution:
delete /var/mobile/Library/Caches/SpringBoardIconCache and /var/mobile/Library/Caches/SpringBoardIconCache-small
then respring 🙂 (no need to remove and reinstall apps)
NOTE: if you have categories installed you might have to uncategorize everything first.
I have the opposite problem though. I have 3 icons that are large and not affected by the Illumine theme. They are ToneFXs, AnyRing, and SBOrganizer. Any ideas? Deleting the icon cache has worked for many icons with this issue except for these 3. It's bugging the hell out of me. LOL