Sonarr does not seem to be noticing qBittorrent

Sonarr version (exact version):
2.0.0.4463
Mono version (if Sonarr is not running on Windows):
4.2.3 (Stable 4.2.3.4/832de4b Wed Mar 16 13:19:08 UTC 2016)
OS:
Ubuntu Server 16.04.1 LTS 64bit
((Debug logs)):
This is after clicking update disks
http://pastebin.com/raw/EHw5WWYc

Description of issue:
This all happened once I put in an external hard drive and rebooted the computer, I’m not sure if it had to do with an update or if it was the reboot or just the fact that I added a new hard drive and system linked some things.

When I originally plugged in my external hard drive I then rebooted the computer and when about using sonarr like normal, at first it worked great and it had all the tv shows and videos filling up my activity log, I then went out for a bit and I came back and saw that some of the videos in the activity bar were stuck.

So I went to qbittorrent and everything looked perfectly fine. I then restarted my computer and now sonarr shows nothing under activity and everytime I refresh the disks it says it doesn’t find anything.

Any ideas on what to start doing to check for issues.

I went ahead and tried something with couchpotato and it worked perfectly fine. So not too much can be messed up.

I was thinking it’s a permission error with the new hard drive but when I type in stat /media/usb0 and stat /media/usb1 I get the same permissions and everything

When was the last time the Check for Finished Downloads task ran (shown on System: Tasks)?

The logs don’t show any errors, but also don’t show that task running (though that might just be due to how much time the log covers).

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