In SimpleIndex 6, file extensions were changed to default to lower case so this should no longer be an issue. If you want to default back to upper case file extensions, you must edit the registry.
Go to HKEY_LOCAL_MACHINE\Software\SimpleIndex\Misc
Create a String value called “UpperCaseFileExtension” and set to 1 for upper case or 0 for lower case.
This registry setting will also work to change the default behavior of version 5.