I tested with and without any mods, and vortex refuses to launch skyrim as AE. With the latest SKSE, vortex is launching skyrim to the regular SSE, where on the main menu it says "Available Now: Skyrim Anniversary Upgrade!". It also lets me try to log into a Bethesda account, which I've never had to do before. When launched from steam the game opens to AE normally. I'm also using the latest ENB version v0.499. I also have a suspicion that this is effecting AE DLL mods, as non-complex mods work fine as well as ENB, but enabling the AE all-in-one address library makes the game stuck on the menu icon when attempting to start a new game.
Some information:
Steam edition of AE
Skyrim SE Version 1.6. 1130
Vortex version 1.9.10
I tried attaching my latest vortex log but it's giving me an (Error code: -200)