Step to reproduce:

1) Create a new .minecraft instance for the game (in our case, just remove the "resourcePacks" and "incompatibleResourcePacks" lines form your options.txt will work)
2) Launch the game, wait for the options init
3) You can see in your options.txt that resourcePacks is an empty list (it should contain "vanilla" because the vanilla pack is loaded)
4) Go to the pack screen and close it immediatly, the game will reload ressources even if you did not change anything because the list of enabled packs on the screen contain the vanilla pack, but the list in the options do not
5) You can verify that "vanilla" has been added to the resourcePacks list in options, and that going back to the pack screen and close it will not trigger more reload

UPDATE:
Found an easy fix. You just have to add "vanilla" to the default list in the GameOptions class constructor.