I do not use hyperspin, but the problem is that the emulator is closing badly and it will not save the last configurations, in the hyperspin forums this is your solution
you could try with ahk commands, or also with closemul
Run,% executable%% romName%,% emuPath%, Hide
Process, WaitClose,% Executable%
ExitApp
CloseProcess:
Send, {ALTDOWN} {F4} {ALTUP}
Return