Looks like your original "bad" cvs import somehow did what you wanted,
rather than what you told it to do, and everything is fine. I tried a
similar cvs import yesterday and it put the files in the wrong place
just we both expected. But somehow, yours worked fine. Why, I've no
idea, but sounds like some additional CVS magic going on behind the
scenes there.
Having your tag named "OACS-4-6-3" only on the acs-automated-testing
package is pretty confusing. You tagged the right thing, you just
picked a confusing name for the tag. So I would put a new tag on the
same spot, named "acs-automated-testing-oacs-4-6-3" or something like
that, then remove the old "OACS-4-6-3". (That way when you later want
to actually import all of OpenACS 4.6.3 you won't be confused about
why you already have an "OACS-4-6-3" tag, etc.)