Please help, I just can't get this working

My brand new Super EverDrive plays most games and saving seems to work on at least a few (Donkey Kong Country, Mario All-Stars). However for Metroid, it just won't work. It will save once, after the intro level and you land on Planet Zebes for the first time. However after that it just won't save. I go and get the Morph Ball and the missiles. I've tried saving at the newly accessible save point in the shaft and at the ship. It just doesn't work.
I stand on the save point/pad in the game and it asks me if I want to save I press Yes/B and the popup disappears immediately. There is no "save animation" that I see in youtube videos:
https://www.youtube.com/watch?v=2mHYOzLh19E&feature=youtu.be&t=12m16s (Although they might not be playing on real hardware?)
I've tried resetting and manually writing the SRAM to the save file, nothing. I've tried using different ROM files, no joy. It is very frustrating that ever time I play I am back at the start :-(
Roms tested (on a PAL SNES):
Super Metroid (E) [!].smc
Super Metroid (E) (M3) [!].smc
Super Metroid (JU) [!].smc
Super Metroid (U) (M2) (VC).smc
Please can someone help? Thanks.