That's a good question, EMS. The robots.txt protocol can get kind of
confusing when you think about it too long, and it sounds like you've
thought about this a bit. However, in this case, it might help to
look at robots.txt from the perspective of the spider.
When a spider finds a URL, it takes the whole domain name (everything
between 'http://' and the next '/'), then sticks a '/robots.txt' on
the end of it and looks for that file. If that file exists, then the
spider should read it to see where it is allowed to crawl.
In your case, Googlebot, or any other spider, should try to access
three URLs: domainA.com/robots.txt, domainB.domainA.com/robots.txt,
and domainB.com/robots.txt. The rules in each are treated as
separate, so disallowing robots from domainA.com/ should result in
domainA.com/ being removed from search results while
domainB.domainA.com/ remains unaffected, which does not sound like not
something you want.
The problem you might have with the setup you have described is this--
in order to keep domainB.domainA.com out of the results, you would
need to have domainB.domainA.com/robots.txt exclude robots, while
domainB.com/robots.txt welcomes them. This means that you would need
to have a way to make domainB.domainA.com/ and domainB.com/ serve
different information, and judging from what you've described, you
have not set up your server to do so yet.
Of course, it is always possible that I have assumed to much about
your situation, so it is a good idea to use Google's robots.txt
analysis tool (see http://www.google.com/support/webmasters/bin/topic.py?topic=8475
) to see if your robots.txt files already produce the results you
want.
If using robots.txt files doesn't solve the problem, and assuming that
you want to continue hosting all of your content on domainA.com, one
strategy you really should look into would be setting up a 301
redirect from the pages on domainB.domainA.com/ to domainB.com/ . If
you need more advice on how to do this with your server software, your
hosting company's tech support would definitely be the best place to
start, but this group is here to help if more isues arise. 
Hope that helps!