[ProjectGSX]

Id try copying new icons for those apps into your theme directory.

Edit - I just installed the Leaf theme so I could try to see what youre talking about .. and all of my icons are the same size. Perhaps the theme did not install properly? Go into Cydia, remove the theme. Return to springboard and let it respring. Then shut the phone down. Power it back up, reinstall the theme and see if you have the same problem.

Also, posting a screen shot of the problem would be useful.

Here is a screen from my phone with Leaf installed. You can see that the theme provides icons for some apps, but not all.. they are, however, all the same size.