Ok I figured it out.
QH (and many other addons) saves locations in the file: World of Warcraft\WTF\Account\AccountName\Server\CharacterName\layout-local.txt
I had locked this as "read only" back in December for this character because everytime I logged in the game was scrambling my chat windows (no idea why, was not addon related that I could tell).
To fix I copied the settings for the QH Tracker from one of the other characters and TADA its where it should be