Hi again,
thank you for all this info! Just a few ideas now:
1. I can't see if the 10 gates in your layout are connected -- but I'd suppose so.
2. Is it possible that your av_extracted view contains each 10 of these MOSFETS (M0, M25) with slightly different names (always with the same 4 nodes), totally widespread over the whole netlist -- and you just found one of them (each)?
3. If not, I'd suspect your extract rules aren't correct.
4. Also -- if 2. is not true -- your LVS shouldn't pass when comparing those two netlists. Then there would be something wrong with your LVS rules, too.
Both rules' sets corrupt? Rather unlikely! But then, I'm on my wits' end, sorry!