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The only thing that I can think of that would be a penalty is a few individual client order pages that link back to the home page. These could possibly appear as orphans or gateways to the spiders, but is it possible to see these pages if they are in separate directories with no links in?
What are the solutions to get our PR back? Do we just wait it out? If I make the order pages visble in the linking structure and add a login system will this fix the problem?
Help!
I would not worry too much, as you have been given a grey toolbar and not the dreaded white toolbar. Your client's site has been removed from the index for one reason or another, and has most likely not been given a penalty.
While waiting for Google to update again, I would work on gaining strong links from other websites that are not your clients.
I agree, the Toolbar can be flakey at times. Even if the problem lasts all of this cycle, then as agerhart points out it's most likely not a penalty. Even a short server or Internet backbone problem can be enough to loose a site.