She only goes back to fix times that the Great Intelligence has misdirected him, so if in the original timeline the Tardis opened the doors to entice him back (as she said she did in the Doctor's wife) the GI might have opened the doors on another one and Clara then had to direct him to the one he'd had historically.

It only means they noticed it was broken at that time. In Logopolis the Doctor notes it was already broken before he stole it, although he still thinks it only actually stuck at totters yard. Also Ian notes it's not working before he enters as the police box is out of place inside the yard. The doctor has managed a repair that lasted for a few trips before in Attack of the Cybermen - so it's possible a similar repair by the timelords allowed the changes that Susan re before it finally returned to its preferred state and stuck again.