Mac needs to repair library after changing location of home directory

I recently reinstalled Yosemite to fix the notorious WiFi bug, and i have two hard drives, one SSD which i reserve for apps and boot, and the other HDD for data (including user data).

I started up my mac made a user account on the SSD (aside from my original one, this is a safety precaution in case the HDD goes down and i need to log in to an account on the SSD), then i copied my user folder to the HDD and went to the advanced settings for that account and pointed it to the new location on the HDD.

When i logged into my account that now has a home folder on the HDD a screen pops up saying OS X needs to repair your Library to run applications. Type your password to allow this

I type my password but it just pops up again in an infinite loop.

One strange thing to note is four ? symbols on the dock for keynote, pages, and other apps that i haven't had installed (And haven't even purchased).

Why would simply copying the fresh user folder from my SSD to my HDD (both were formatted during install) cause this error?

When i force restart and log into the admin account on the SSD i can point my user folder back to its original folder on my SSD (since i did not delete it) and then log into it and everything is normal (and there are no ? symbols for apps i don't own on my dock either.