This glitch happens when you use a combination of either tp'ing, switching gamemodes, or a combination of the two. I will be trying to find out exactly what causes this visual glitch to occur, and when I do, I will add a new video to this description. For now I will show you what it does (this is a client-side problem).

When switching out of spectator mode after the glitch occurs, your player skin acts as if it is still invisible. When looking inside of the inventory, the player model looks translucent like the model of the player head while in GM3. You also cannot see your player model's arms if nothing is in your inventory. The armor bar stays exactly the same from what armor you had leaving GM3. Switching gamemodes does not change or fix anything, and from what I've found, both rejoining the server and changing worlds makes this stop.

In the video, I am on my Vanilla 1.10.2 server using command blocks, and when I use the tpHome trigger, it is bringing me into the end and back to the overworld (using the bed mechanic with /spawnpoint).
Link: https://www.youtube.com/watch?v=op05NDaoq0Q&feature=youtu.be
Video will finish uploading within 20 minutes.