[Hiphopopotamus]

I just installed that build and it stopped my video libraries form showing. Music was still there, but TV and Movies was empty. MySQL setup, not skin related as I switched to confluence, and it only had "Video" header, no Movies or TV anymore. I reverted to kodi-20151003-b2e2eca-master-armeabi-v7a.apk and all good again.
I rebooted several times before reverting.

working flawlessly for me. What was your previous kodi?

That's happened to me in the passed. your TV and Movies are still there you have to set TV & movie scraper again.

EDIT: I just installed the 26th build - kodi-20151026-6b91dde-master-x86_64 - on my macbook, and same issue.

kodi-20151003-b2e2eca 16.0 Alpha 4

I know they are still there, as soon as I reverted to the version above, they were back. With the MySQL setup, and advanced settings xml, I shouldn't ned to scrape again, it should be recognised immediately.

I just did a full system reset/erase and decided to start by installing the latest nightly - kodi-20151025-c524791-master-armeabi-v7a.apk and got the exact same problem after doing the full set up and setting the video sources and asking it to scrape and create the library. I then installed kodi-20151003-b2e2eca-master-armeabi-v7a.apk and it was all good again. For me the 17th, 23rd and 25th nightly builds all have this same problem.

The skin I use SiO2 wasn't listed as available, so I did also try to install the 15.2 build - kodi-15.2-Isengard-armeabi-v7a.apk and it wouldn't let me.

EDIT: I just installed the 16.0 26th Nightly build kodi-20151026-6b91dde-master-x86_64 on my macbbok, it has the same issue with the library getting removed.