Yep, I’m running into this same thing. It’s causing a MAJOR pain in my butt. Using any of the Libretro-based emulators in combination with my Tankstick (using the XArcade2Jstick service) gives some VERY odd button and keyboard defaults that are entirely unintuitive and unsuited for the classic games I like to play. Each time I boot the emulator from the menu -basically every time I select a new ROM! – I have to redefine everything.
I wish we had some indication this is being looked into, or might be fixed in another Beta. For that matter, 3.0 Beta 2 has been out for a good while. Has anyone seen any indication of a new release or possible 3.0 Final that would fix this bug?