You won't see the storage area while you're connected in mass storage mode. When you connect in mass storage mode, it makes the devices available at a low level to the PC. This means they can't also be available on the N900, so get unmounted.

If you're not in mass storage mode, you should be able to see the partition mounted on the N900, otherwise you should be able to see it as a drive on the PC. If you can see it okay, and it shows enough space, then it must be a bug in Map Loader.

I've seen some apps which appear to be using too small variables for checking available space - if you have over 16G free then it discounts the first 16G. If this is the case, you could try putting data on the drive to take it below 16G free, then see whether this makes a difference to Map Loader.