Please use the dll loader in the meantime. SKSE64 for AE is currently lacking plugin support. It's a plugin I made that re-enables achievements while using mods by patching Skyrim SE during runtime. REQUIRES THE LATEST VERSION OF MY DLL LOADER TO BE INSTALLED IF YOU ARE NOT USING SKSE64! You must install via NMM, or manually or use the SKSE64 version.
The dll loader version does not work with Mod Organizer.