Are you talking about a stand alone mobile version or one where there is a link on your full site saying something like "click here for mobile friendly version?" I have done several mobile friendly sites which are a part of a regular site with a link as described above. So far, all the SE's have had no trouble indexing them. However, WMT often tells me I have duplicate title and description tags, though it does not seem to have negatively affected anything.
I suggest you put this meta tag in your mobile pages. I think that may be why the duplicate title and description tags are not an issue:
<meta name="HandheldFriendly" content="true" />
I would also suggest creating a mobile sitemap though so the SE's can distinguish your intent. If you have never done one before, here is the layout: