In the new version flash size is automatically detected for some games, and Pokemon games are happy when they have 128KB flash. I suppose this is a problem, and when you want to load a game from previous version a message appers: "Configuration of loaded state differs from the current one. Mismatch in gbaMem.flashDevice". Is it true? To make it work: select a game and go to "Advanced Launch" page and select "Macronix 64KB" flash. Click on "Run". The options from "Advanced Launch" are saved in states, so save game once and you don't need to change things in "Advanced Launch" again. Please next time be precise, write which version are you using and write exact message which appears, and what exactly happens, I don't want to guess every time. Thank you.