I kinda figured that out, and really it's not an issue to force them to 16mb like that since I save on the USB anyway, I'm just pointing out that for those who use usb loader gx and have one of more games they wish for them to be saved individually to start the save with nintendont first, I did that and everything worked just fine!
The thing is that you don't need to do that, just open LoaderGX, go to settings, Loader Settings, scroll down and change MCEmu to Individual. Done, you have a single memory card for each game, and after my tests I can confirm it's only 2mb on size.
If you'd rather have Multi, just set MCEmu to On, and play like that, using a 16mb memory card for all the games. If you ever find a game that doesn't get along with it, you change the settings for that game to Individual, and that's it.
If it's saved individually, they don't need to start the game with nintendont first.
USBLoaderGX is using the card size defined by the user for individual save.
I'll wait for Faku's test to tell if there's an issue.
I deleted a memory card i had for Resident Evil Zero (as I didn't start playing that one yet).
The first time I had the global settings as Individual and 251 blocks, loaded the game, formatted the memory card and exited. The file created was 2mb and so i deleted it once more.
Then I changed the game's setting to Individual, and left the block size as Global. Again, i ran the game, exited, and the file was 2mb.
Finally I changed the global setting to On, and left the game's settings as Individual. There were no issues and the file was 2mb on size.
My guess is that either sonictopfan got confused because there was a previously created ninmem.raw, or he accidentally changed the setting to "On" instead of Individual... Either that or he set a bigger block size and didn't realize what it was.
Edit: Made a final test, changing the block size to the max value and then i did get a 16mb file, so I guess everything works as it should.