I think this is probably a case of Size versus Size on disk here.
Apologies if this is a little unclear, but still
The underlying filesystem on your disk is made up of lots of little 'bits' called allocation units. The standard size for these in FAT32 filesystems is 32kb
Now for technical reasons, a sector can only be assigned to one file. Now, your files are highly unlikely to end on an exact multiple of 32kb, and thus every file will end up taking anything up to 32kb extra.
There are also a couple of other cases that work in a similar way, all in all that means that each file's size on disk is actually bigger than it's size.
What does this mean?
The more files you have, the more of these missing kb there are
A rather extreme case in point is attached from my system.
-Leezer-