Definitely thrips, evil bastards, hate them more than you can imagine, love to munch tender seedlings and low leaves since they breed in the dirt and then the larvae climb up stems to the first leaves they find... EVIL EVIL EVIL!!!!!

Neem is good to protect older plants as you said but you might have to water your pots, ALL OF THEM, with predatory nematodes if you want to kill them organically.

Or you can just bug-bomb with pyrethrin once a week for 2 or 3 weeks and use yellow sticky traps to catch the stragglers.

Did I mention how much I hate thrips?