If you can execute bash scripts on your server, you can translate everything to lowercase easily with this one-liner.

for i in `find * -depth`; do (mv -fi $i `echo $i | sed 's%[^/][^/]*$%%'``echo $i | sed 's!.*/!!' | tr [:upper:] [:lower:]`); done

It will work recursively, and it will rename everything to lowercase.
So anything you have that you don't want to be translated, be sure its not anywhere within the directory tree that you run this from.