Thank you all for having patience with me. Think I've finally figured out where I was wrong.
I continually tried to use the Desktop shortcut, running that as a admin, which didn't work.
Using the IN-FOLDER eq2.exe on the other hand helped, the patcher for the launchpad itself downloaded ALOT more then what it did before, and it is currently in the process of scanning files as I type this.
Hope it doesn't stop at that though.
*EDIT* Correction, it has started downloading all the needed files
Thank you all for the patience and help, just 7½ hours to go till I can play now...
*EDIT*