I've got the same problem too. I used matte nano and then tried illumine and decided to switch back to smoog but some of my icons still remain small. Is there a fix? Even if I try other themes it doesn't do anything. I tried deleting illumine but sadly it didn't do anything
i found a solution to this all you have to do is uninstall and reinstall them. For apple apps its easy you just delete and resync from your backup but with cydia appas you will have to uninstall and reinstall.
I must say this is completely irresponsible of the Illumine developer. A fix should be something they worry about!
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