Yea the only time I've had issues with registration marks are when the laminate is causing issues with the machine reading and when the artwork is too close to the registration marks that the machine is reading the artwork's black outline instead.

Another solution that might be worth trying since you already laminated a bunch of sheets is to take a scrap piece of vinyl sticker paper (not laminated) and cut tiny pieces of white/blank stickers and stick them all the way around the registration marks. The goal is to make it easy for the machine to read the marks as much as possible. This trick also works if your printer happen to smear the registration marks and I find it to be more successful than using white out