I have made an update to webassist/file_manipulation/helperphp.php that I have attached.
Please upload that file and then you can use:
[FileNameLower or [FileNameUpper] in place of [FileName]
That will force the file name to be all upper or all lower case when saved so you wouldn't ever have any case sensitivity conflicts.
I've also updated this file in the latest build, so if you reinstall it will be used on future applications.