Ran into other issues:
My Valin attacked Orthus, who was occupying a barbarian city that originally belonged to Sheim. I seen 4 dots over the city so, I moused over to see how many additional troops there were and it was just Orthus, a worker, a barbarian spearman and a "magical item". I figured it was Orthus's ax so Valin attacks, kills Orthus. Next round, kills spearman and takes city. Alas, no ax, so I razed the city...still no ax. This is happening every time since patch D and only happens when Othus is over a city. If he's mobile, I get the ax. Also, I played a game without patch D and I don't have this issue.
I also noticed that the Minister appears in the weirdest places. I actually had a game where is was located on 3 different continents at the same time, and this was at turn 287. I usually know this is happeing ahead of time because civs that I found while exploring the seas will not trade maps. When I do find a civ to trade with (usually costs me multiple techs), I get a picture of the entire world and nobody has researched Optics. (??). I also had a game where I explored my entire continent, killed my neighbors (as always) and he appears later as a barbarian archer in a barbarian city.
I did submit a saved game on a previous thread, if you want to see what a really weird game looks like. Lastly, I want to reiterate that this is only happening since either patch D ( I don't have any other patches saved) or since the patch that let you choose Random Good, nuetral and evil civs. I say this because patch A worked fine and I didn't add another patch until D came out.