Thank you for the suggestions! After contacting Google they didn't get back to me but the issue seems to be fixing itself after 3-4 days.
I'm still monitoring as I'm not sure if it is totally fixed. When I first typed the OP, 40% of my pages were affected, the next day, 80%.
Today, strangely, less than 10% of my pages are affected. The site is ~ 6 months old but I placed adsense on it only for around 2 months. My adsense account is however more than 5 years old. (The issue is only present in a specific domain.)
I'll carry on monitoring and will post if the issue doesn't fix itself!