Normal procedure when repairing wheels, would be to aluminium weld to fill the missing bits ,file and sand it down,apply aluminium primer(yellow stuff), paint and finally two coats of varnish.If the guys that done your wheels did not apply Aluminium primer,your stains could be a late reaction to the lack of it!Also,if the varnish they used is of poor quality,you would also get sort of yellow stains after a while!
Hopefully ,the stains within the wheel surface, could just be on the surface of the top varnish coat!You can easily test this by using a 1500/2000 grade Wet Sand paper(use with plenty of water)and see if the stain comes off.The surface will be dull,but dont worry because you can easily polish it off later(I have used this method successfully even to highly polish dull and scratched BMW plastic headlights)!To take out the dullness on your wheel surface you need to use something like "T cut" colour restorer (been using it for over 20 years...great stuff in the UK!)which we use to take out surface scratches and then you can "zaino" polish it to give it the wet look!

It could also be some type of industrial fall off but then you would also have it on the rest of the car!!