So it's the same problem on new version for save (for the sound bug too), I didn't try blastEm trick, I will test it, I need to find it and install first (it will be the linux version I only have linux for test it)
I found something I didn't saw before in everdrive's menu. If you go in the folder mega directly from megadrive, there is save, snap and txt options available. I selected save and they ask me to copy from sram to sd or sd to sram but even with that, after starting MD tracker it's still says generating module data and it's empty :-(
EDIT : I tried with chmod 777 to save folder and files but the problem is still here. I saw that the save file name.srm have spaces in it. Often programs don't like it, maybe it's something like that? But it should not be that because it's good created...