Let me preface this by saying I don't want to run the Cleaner unless absolutely necessary... reinstalling InDesign, Illustrator and Photoshop and all the extra crap like AIR just to fix the one app is ridiculous.
Anyway, previously Illustrator was installed to an external drive that no longer exists, so now it forces to install to the old directory.
This is still the case if I download the manual installer instead of through Download Manager.