Finally had a chance to try the latest update & menu, I still had to replace the TOP file with the earlier version but everything seems stable in regards to no graphical glitches or crashes when writing to the slots.
I do have a slight issue when usually booting the cart for the first time though with this firmware, it will fail to load some graphics, I can tell this has happened as the Unibios screen will fail to load the NEOGEO text then the game boots with missing graphics, if I turn the system off and back on it's generally fine after this.
Also enabling most cheats in the Unibios will cause games to crash, freeze or have graphical glitches in the few games that I tried i.e The Last Blade, Art of Fighting 3