I get the same results, and the drop-down box in the Explorer format dialog does give different allocation sizes for a 2GB vs a 4GB card.
It will work with /FS:FAT if that's any use? I dunno what the requirements are for Minimig. Also I'm not sure if this is a literal spec thing or more down to Microsoft's generally conservative filesystem limits. For instance FAT32 partition sizes are artificially limited to ~32GB but some third-party apps will format them up to the real maximum.
-Edit-
Tried another util that *will* do FAT32 up to 2TB, but still won't get round the clusters issue so I'm guessing it is a hard limit.