I got a bit confused but now I think I know whats going on...
When Gateway creates a .sav file, it gets the correct created/modified date set in the file system. However, when new data is written to the .sav file (i.e. when you press home, x, a), the "date modified" of the file does NOT appear to change.
I noticed this with my Zelda save file (00040000000EC400.sav). At first I thought Gateway was failing to write my new saves to the SD card, storing them only in the gateway cart. But, actually it seems to be working fine. Phew!