multidata is turned off, so I strongly assume it is just case sensitivity. And I fear that is something that can't be simply turned off as it influences the whole file system.
As a side note, I think Freespace downloads all files in just lowercase, at least the few files I received were all this way.
Can you affirm that, and if, can that be changed in the code so at least the downloaded files have the correct filenamen?
(Next problem would be, as Windows doesn't care about case-sensitivity, many users don't care about it, either, and the *NIX users still get files with wrong names.)