[jvandenbroek]

http://xbmclogs.com/p3hlv3yxk

I hope this is what you need.

Could you try rename /storage/.kodi/addons/script.afterwatch-0.9.4 to /storage/.kodi/addons/script.afterwatch and then restart Kodi?
It seems that Github includes the version number, which isn't intended. Not sure if it wouldn't work than, but it's worth a shot. Also just set the 'assume as watched' to 90 for this test, could be some mathematical error when set to 1.

I'm adding more debug options which could help find out what's going on. But I'm curious if renaming helps!

[edit]I see that you're using the watchdog add-on. Could you (if above doesn't help) try disabling this service, restart Kodi and retry?[/edit]