I think it is strange that nobody else has had this..
I tried different things, and found a way around this.
If I change the resolution before loading the level, the enemies are activated.
So I changed the ingame resolution from 1024x768 to 800x600, then started level 1 and the enemies were all active.
When I reload the game, the game is still set to 800x600. This time the enemies are inactive again.
Again, I restarted and changed the resolution back to 1024x768. The enemies were active.
So if I change the resolution before running the game, the problem is gone.
However, I should really change it. Just scrolling through the resolutions and selecting the same resolution again didn't work.
I tried different things, and found a way around this.
If I change the resolution before loading the level, the enemies are activated.
So I changed the ingame resolution from 1024x768 to 800x600, then started level 1 and the enemies were all active.
When I reload the game, the game is still set to 800x600. This time the enemies are inactive again.
Again, I restarted and changed the resolution back to 1024x768. The enemies were active.
So if I change the resolution before running the game, the problem is gone.
However, I should really change it. Just scrolling through the resolutions and selecting the same resolution again didn't work.