I had the same problem with a Floyd Rose classic strat in vintage white i bought new about 10 years ago. After a few months i had grey patches all over the back, never sent it back because it took me 3 months to get and that came with a fender moulded case.

I wonder if its possible that the paint wasnt fully cured.Just a thought.

mine was brand new, probly never saw day light when i had it, just over a short period it slowly went grey underneath the lacquer. glad it was only on the back though.

I would suppose that the case itself might be the problem too. Long ago I had a case that never quite lost the sickly sweet smell of the hide glue used to adhere the fabric. Anyway it might be possible that something in your case was gassing off, and reacted to the finish on your guitar. not saying that actually is what happened, but it could be a possibility.

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I'm not an expert, but I play one on the internet.

It doesnt bother me that much anymore, gives it a "worn in" look, a bit like my dads 79' strat which has a "worn out" look