Hi,
Maybe you are using a linux network share to host your files, but on windows the file system is not case sensitive like it is on linux. It is not possible on windows to have two files in the same folder with the same name differing only by case. This is a feature of the operating system beyond the scope of any control by mojoPortal. By default mojoportal is going to lower case the name of any image files uploaded via the UI. Possibly if you uploaded an mixed case file by ftp and then tried to modify it or upload it again with mojoportal it might cause an error, but I would be surprised if it resulted in 2 files on a windows drive that differ only by case of the file name, I would expect it to overwrite the file since from windows point of view it is the same file.
Best,
Joe