These files are not in root, but in the \EFI\Boot folder on the VTOYEFI partition (which is often hidden).
I've never had this problem, probably because all my isos are in a \Iso folder and this directory has been specified in the appropriate Plugson section. In my case, i think that Ventoy only scans this folder.
Try changing the setting (change the option from 0 to 1) of the VTOY_FILE_FLT_EFI item in the Plugson menu. I think this should solve the problem.
I've never had this problem, probably because all my isos are in a \Iso folder and this directory has been specified in the appropriate Plugson section. In my case, i think that Ventoy only scans this folder.
Try changing the setting (change the option from 0 to 1) of the VTOY_FILE_FLT_EFI item in the Plugson menu. I think this should solve the problem.