The argument came about several days ago when Disney wanted to renegotiate their current terms with various cinema chains around the country. The new deal would give Disney a great portion of the revenue from box office returns not just for Iron Man 3, but many of their other upcoming releases as well. Needless to say, movie theaters chains weren't exactly okay with this new deal and AMC and Regal have decided to fight back against it.
At this time, 3 of the largest movie theaters chains have ceased online pre-sales of Iron Man 3 tickets, until a resolution can be agreed upon between Disney and the theater chains.
While it is possible that Iron Man 3 wouldn't be shown in those theaters if an agreement isn't reached, chances are they'll get it sorted sooner rather than later. Seeing as how it's going to be one of the largest money-makers to come out this year, I don't see either side wanting to drag this out any longer than they have to and miss out on potential sales. Even so, it's a scary thing to consider.