The resource pack I use (The Classic Texture Pack) in my global resources doesn't stay active when relaunching the game. I guess it's related to the Marketplace as that's the only resource pack that does it when the other active ones were downloaded outside of the Marketplace have no affect from this issue.

Steps to copy:

1. Have a resource pack purchased from the Marketplace
2. Activate the resource pack in your global resources and let it save
3. Close and relaunch the game
4. Check the active resources to see if it's still there and active

Every time the game is relaunched, it throws the resource pack into the inactive resources tab.