By default, saves on the 3-in-1 are offset 64KB into the SRAM. In order to have saves for both the PSRAM and NOR games in SRAM at once, the 3in1 Expansion Pack Tool switches the SRAM page when it runs games from PSRAM. Saves for games run from PSRAM are offset 200KB into the SRAM. Saves for games run from NOR are left at the standard 64KB offset, so you can boot the game in NOR from the DS or flashcart menu and the save will work.
The problem with the EZ4 Client is that sometimes it forces games to switch the SRAM back to the default page, even when it's not necessary. This has no effect on games run from NOR (they use the default page anyway), but it completely circumvents the 3in1 Expansion Pack Tool's method of dealing with multiple saves. When this happens, a game run from PSRAM will overwrite the save for the NOR game, and the PSRAM game's save will not be backed up because it's not in the right place.
Once again, this problem only affects games that are run from PSRAM with the 3in1 Expansion Pack Tool. GBALdr, the EZ-V, and (as far as I know) NDStation do not keep multiple saves in SRAM, so they are not affected.