After searching everywhere possible I found something that works for me.

Theres 3 things you will have to do.

1. Follow the instructions here written by swampthing (THANKS!). Link: https://forums.stardock.com/368958/page/1/#2448655

2. If your shortcut icons are missing (.lnk files). Use this registry patch to fix them. Link: http://www.winhelponline.com/fileasso/lnkfix_vista.zip (Works with Windows 7 too.) Got that from here: http://social.technet.microsoft.com/Forums/en/itprovistadesktopui/thread/e8631c28-4ce5-43cc-8865-b75fa2255b57

3. Once finished restart windows. Everything if not most of the icons should be fixed. If not all is fixed, read step 4.

4. Look at your backup.ini file located at: C:\ProgramFiles (x86)\Stardock\IconPackager (Or similar depending on your system). See what icons need to be fixed in there and fix them by going back to step 1 and performing them tasks.

Hopefully this helps people in the future. Thanks for looking.