> Area 51 (Time Warner License) [folder: area51t - parent: area51 - size: 2mb]

You have to merge the chdfiles, too. For example put the area51t.chd in the area51 rompath subfolder.
...or don't use subfolders for the chdfiles at all.

Generally look out for some clonename.zip files or clonename rompath subfolders and remove them.

Roman Scherzer
ClrMamePro