I always look at these things the same...
If you have more than one site linking to other sites, ensure they are on a different server. OK, perhaps I am being overly cautious here, but knowing what Google can be like, I would not take chances.
If there are no links between the sites, then as long as the content is unique (as you say it is), then you have no problems from a duplication point of view. If each site serves a different purpose, there should be no problems.
I would need to look at the sites to get an idea why Panda hit them - there are so many possibilites. The main ones as we know though were thin or duplicate content and adverts.
Is there a possibility your content has been duplicated somewhere else?
Andy