If the www version is the one you want and the penalty has been revoked I wouldn't think you have much to worry about.

If it were me, I would still submit a reconsideration for the non-www and kindly explain the situation - namely, how the penalty was revoked for www and you would like the same for the non if anything, but for peace of mind.

Is the preferred domain set or just a redirect?
So one version still has a message in manual action and the other does not?
Which version is indexed or s it a mix?

Shai... good point. You will want to make sure you have the www version set as preferred in WMT as well as a 301 in your htaccess to www. I just assumed this.

Make sure you update the thread so we know how this turned out. In the past I have noticed little things like the screenshot image not updating on my non-preferred domain in WMT and this may be the same case with your penalty removal. Maybe they queue the non-preferred updates rather than them being automatic? You might also want to make sure the page isn't cached somehow in your browser (I think I remember something like that happening to me in WMT as well).

Shai,
Preferred domain is set to www and non-www redirected to www.
Site is not indexed with any non-www URLs.

On the same day www version received a message to the effect that penalty was revoked, non-www version received a message that site still violates. A far fetched idea could be there are some poison links pointing to non-www, but then I would assume Google not to lift penalty from www.

mihomes - There were two separate messages, one to www and one to non-www. It is not a cache issue.

This is really interesting... your incoming link profile... what portion of incoming spammy links would you say go to the www and non-www?

what portion of incoming spammy links would you say go to the www and non-www?

When the links were removed/disavowed, they were removed unmindful of whether they point to www or non-www. So, what remains now are those that are assumed to be non-spammy. Any links that remain to non-www, which Google thinks may be spammy, we can't be aware of.

This is very strange. I just checked two penalty removal clients and both have the penalty message on both the www and non-www. In both cases, the vast majority of links were to one or the other. One client that had his penalty revoked a couple of days ago, has had both instances of the message disappear (www and non-www). This insinuates that Google does not differentiate between the two for penalty purposes. Your case is definitely out of the ordinary.

If I were you, I would just fill out a RR on the non-www site explaining the discrepancy. I almost guarantee you that you will get a penalty-revoked message on that one as well within 8 or 9 days. I would also mention that rankings have not improved at all, sometimes, that can cause them to nudge it a little. ;)

Please keep us informed on how you get on.