Library not showing after update, taking hours to update

[Sharon]

release version: 0.4 (build: beta-20160313)
RPi 3+ ifi 5V, 2.5A psu + Schiit Modi + 2T Hdd connected via router (with its own power source)

Hello,
Some issues which I haven't been able to resolve, would appreciate some insight:
1. Updating the library takes a few hours, I have about 1T of music on it in three folders
2. While updating I can play from the music shown in the "Network Mounts", with clicks and lags
3. When finished updating, the "Network Mounts" is empty again

I can see the albums and artists in "Browse your Library" --> "Albums" / "Artists", but when adding to queue, there is no sound. I can listen to web radios added to the queue.
All files on the Hdd are either music files, album art (.jpg) or text files (some are in non-standard fonts but it reads them just fine)
The same behavior also when the Hdd was connected directly to the Pi. After updating, the "USB Mounts" would show empty, while updating it would play with clicks or completely crash.
Same behavior when trying to access runeaudio through http://runeaudio or through MPDroid.
Tried multiple reboots, multiple sd card flashes with no luck.

Thanks for reading and for any helpful feedback

[hondagx35]