2500 rds thru it ...is only 100 boxes ...so its barely broken in .../ the firing pin spring ...and the head of the firing pin can't be worn at this point ...( I have a Benelli Super Sport / with the same mechanism ...that has at least 10,000 shells thru it with no issues ..).
The mechanism on the Benelli is so simple ..and so easy to clean like you say ..that its hard to imagine that anything is wrong there. There is literally no way to get the spring in wrong / or the retaining pins in wrong ...after cleaning.
I think its a primer depth issue on the shells ...even though they're new. I just can't imagine anything else being wrong ?? I would chalk it up to ammo problems ...and see if it goes away when the current cases of ammo you have are used up.
I would still take the gun apart ...and certainly clean and lube everything ( I use Break Free on the firing pin spring, on the bolt and on the receivers rails )...they shoot so clean, that a little extra lube vs dry isn't going to hurt anything. As long as you're not shooting skeet for competition, where the malfunctions will hurt your scores...I'd just shoot up the supply of shells you have currently ...and see what happens.
If the problem persists ---I'd order a new firing pin spring / and carefully inspect the firing pin ( with a magnifying glass ) and make sure the head of it is not eroded ..and maybe order another firing pin. Worst case ...replace both the firing pin spring and the firing pin and see what happens. ( its not a bad idea to have a spare spring and firing pin anyway - if its a primary gun for you ). Your local retailer should have them or can get them or call Mann & Sons.. at 618-357-2911 and they should have the parts ( they're in Illinois - and seem to have most parts for Benelli that I couldn't find elsewhere - different recoil pads, different comb pads ...that I couldn't find locally.
If you buy a new firing pin and spring ...check them against the ones in the gun now ...to see if the firing pin is worn or pitted...??
I don't know if the gun is still under warranty or not ...but you can call Benelli USA and find out / see what they suggest.