I agree with you, the shuttle has me wondering.
Before, Whistler talked about how everything you did during the work day seemed meaningless and was forgotten. If that happened throughout the day, wouldn't all these employees be useless? Would they not be useless from one day to the next if they forgot the project they've been working on for weeks?
Perhaps the shuttles are the answer. They have an out of the way facility - for lots of reasons - but that allows KS to force everyone to take a shuttle. Maybe there's a spell in place on the shuttle. Maybe the driver performs it, or at least is the source of the magiq, which would explain a humanly error of no signal light, and they could easily spread it to encompass the police officer.
On the way home, there's a spell to make you forget everything you saw so nothing gets leaked, or even implant false memories. On the way there, there's a spell to help jog your memory so you can do your job. It doesn't happen all at once so you wouldn't notice it, rather a trickle throughout the drive.
At some point, Whistler became immune to it. I want to say because of the head injury, or maybe there was magiq involved when that incident happened. That would explain the two sets of memories: the real ones, and the false ones implanted. Now, he isn't affected by any newer attempts to help him forget, but he still has what ... years? Of memories to sift through and figure out which are real and which are fake. That has to be incredibly difficult to say the least, nevermind make you question everything around you - including yourself.
Lots of maybes for my shuttle theory there, but I also think we should open up to Whistler, because like others have mentioned he probably feels completely alone and afraid. If not for 'the cause' then just to be decent human beings.