When I clean my alloys, the spray-on wheel cleaner chemical gets on the brake calipers and discs.

 

The next two 'stops', the brakes don't work as well, but then they're ok.

 

Could the wheel cleaner cause any other damage - soaking into the pads, washing away grease or damaging surfaces - it seems like strong stuff?

They probably didnt work because they where wet, or the chemical you had was oil based.

 

Once the pads make contact with the disc a few times it will burn off most chemicals.

 

Wash your car and get the discs wet. Leave it for 2 hours and they are rusty as hell. Drive to the bottom of the street and the breaks will be crap until the pads have worn off all of the rust. Its probably the same with the wheel cleaner

 

I really doubt that the company would create anythig which would damage braking system.