RE: Mossberg 500 problems?
The only advice I have is take the scope off the reciever and get a cantilever mount barrel. Mounting a scope to the reciever of a gun with a removable barrel is never the most accurate way of going about things.
That being said something sounds fishy. I would go back to the gun shop and ask them about it. If it was bore sighted it should be fairly close from the get go. And the really confusing part is it is the same amount with both guns? Maybe you need a new gunsmith?
How far off is it at 25 yards?