Yes, there's a definite problem. I'd say don't start making any changes yet - the jury is still out, but we'll have an answer you can count on very soon. I;m actively looking for moderators who use iframes in a site and we'll let you know.
I don't currently have any iframes pages, so I'm not 100% certain about the search engines questions - but I'm looking for some authoritative input for you. If there IS a problem, it would only be for original document -- the one that's loaded with the src= attribute. Links to iframes (with a target="iframename" attribute) most definitely DO get indexed.
And it sounds odd to me that there's a problem at all with Google, from everything Matt talked about in Boston. Google bends over backwards to find every link they can - and this one is a no-brainer.
Plus, we've had several members say that Google sends traffic to their "orphaned" iframe document, and looking for a way to fix that. How could they be having that problem if Google didn't index the page in the first place?