James,
1) That whole 'using dots in folder names' has bugged me for years. It's just not right. However, I'm sure that application has you over a barrel and won't let you rename those folders. Have you tried, in your wildcard statement, *.vbs\s\*.* /SUBDIR or *.*\s\*.* /SUBDIR
2) Are your sure the \\CLEAR3\D: thing really works. Normally when you use a UNC to back up files, the drive letter has a $ appended (instead of a colon). This is because, by default, the logical drive letters are not shared openly but are shared in a hidden mode accessible only by DRIVE$
3) Have you tried using three seperate includes where you define the folders explicitly?, e.g., \\CLEAR3\D$\Clearcase_Storage\VOBs\Logger.vbs\s\*.* /SUBDIR
and so on for Projects.vbs and 3rdparty.vbs
This way, BE would run right down the path, saving time, backup just what it needs, then moving on to the next .vbs folder struct. This, of course, is only good if Logger.vbs, Projects.vbs, and 3rdparty.vbs remain static and the only three subfolders of VOBs you intend to backup.
Sorry to be so verbose and I hope some/all of this will help.
I'll process further and if I come up with anything profound, I'll post.
Have a great weekend.
best regards, mike