The "DirectoryName("$*")" line in the standard MyDefrag scripts will cause any directory with a name that begins with a dollar, not to be placed in the zone for regular files (zone 5), but in the next zone (zone 6). There are several things you can do, for example change the line into something like this:
or (DirectoryName("$*") and not(DirectoryName("$")))
Note: you will have to do something similar for SelectNtfsSystemFiles().