1script - 7:42 pm on Apr 6, 2013 (gmt 0)
@netmeg: I don't think it's quite THAT simple. I've never actually submitted non-www version, it always appeared by itself. In other words, a domain and a host (www) are separate entities in WMT but not even quite independent as the standard would suggest. I imagine it's totally possible that the penalty is applied to the www version only but then, since there's site-wide penalty, it's not that big of a stretch to imagine there may be domain-wide penalties, too. I think we also do know now (confirmed by MC) that there are also webmaster-wide penalties, too (i.e. they ax all *your* sites). So, yeah, we are swimming in the ocean of penalties and it would be great to have some understanding of what is it you're asking them to remove.
Anyway, I've submitted it for www version, we'll see what happens.