Playlists/HDD disappear from Kodi when it runs on startup

Hello everyone,
I have Kodi installed in the newest Raspbian Jessie Pixel.
I created audio playlists and installed musicbox and pandoki.
Kodi is set to start on boot BUT every time I boot, all my plugins, playlists and even my external HDD with all my music goes missing.
I must exit kodi to Raspbian, then go back in Kodi and now all my playlists etc. are visible.
**At first I thought it was because I accidentally unplugged my RPi without shutting it down, so I reinstalled everything from scratch. Issue persists.
It is kind of annoying having to go to SSH to start Kodi before I can use the KODI remote control app in my android.

Any ideas?
Thank you!