Ah yes it doesn't exclude clones, may have to revisit that. The original purpose was just a pkm folder (only uniqueness is filenames) which allowed clones to be searched and deleted if requested. With the addition of loading from saves (and now the backup folder), copies upon copies.
If you remove the "#define LOADALL" at the top of SAV_Database.cs and recompile the program, it will disable loading from the backup directory.
I can probably revise the loading routine to automatically exclude clones from backup save files...