Yes mate, sounds exactly like the stains on mine:( (same side even). They were there when I bought it 3 years ago so I’ve no idea what caused them. As you say though they do seem to be under the paint so are probably going to be a :pig: to sort out.

just 2 hours ago i had to clean the dirtiest back wheel i'd ever seen. a combination of sticky chain lube, grit and road tar was shifted by using a hand wash-mitt, very hot water, loads of fairy liquid and a bit of elbow grease. good as new now :)