If you take a snapshot of a game that uses firmware in 6128 or Plus mode, it won't run in 464 mode and vice-versa. This is because the V1 SNA doesn't keep track of which ROM sets are loaded. But V1 and V2 should work in almost all emulators. V3 on the other hand keeps track of exactly what memory and ROM settings are being used so should always work on WinAPE without changing settings. I think the only other emulator that even attempt V3 SNA is Arnold, and I've yet to give Kev all the information on what the extra bits are I've used to attempt to ensure the V3 SNA always works.