that sounds about right,i always clean the rim with a wet cloth and then dry cloth to finish and check my tyre and walls at at the same time,the big question do they stop the bike?I assume these are rim brakes. I'm no expert but if they weren't squealing/squeaking before the clean may be you have cleaned away something on the surface of the rims/brake pads that was reducing the braking efficiency but keeping them quiet. May be you have coated the pads with something from the cleaner. Either way I'm sure they will recover.
Now they are clean you could check the toe in.