Update:
Checked my plugins and deactivate it one by one. Couldn't find a difference. I only found something very strange.
When I change the status of one "confirmed" subscriber to "non-confirmed" and sent him the activation link again, everything works well. The link have the correct syntax. It only don't work for new subscribers.
I'm running out of ideas but I would like to solve this problem. My last idea would be to try my oldest backup and pray. Otherwise delete and reinstall the plugin.