This is happening to me also in macos (with Steam). But it was also happening with 1.1. If you completely exit then all of them are lost. It only happens when you restart the game from inside the game (mod changes or startup changes). Apple M1 Pro 0.000 2024-10-26 17:45:14; Factorio 2.0.11 (build 79...

The same thing here. I would say that it always happens when I start steam on the first achievement. If I restart the game the achievement happens the steam popup comes and everything is fine.
Its not that it crashes. It just stays unresponsive, therefore you have to kill it manually.