I've had the same issue, I found a quick an easy fix.
It seems after you make the icon pack, IconPackager deletes a bunch of the icons and applies the rest incorrectly.
Here's how I fixed:
Make your icon pack, and save as.
- Go to C:\Users\Public\Documents\Stardock\IconPackager
- Select your icon pack folder, and right click it
- Click 'Properties'
- Click the 'Security' tab
- Click 'Edit'
- Now, under each Group/User, you need to check the DENY box next to 'Write'
What that does is it prevents IconPackager (and anything else) from deleting anything or rearranging.
Not the best fix, but it works.