It is probably due to the fact that you already have a site content type in use that you want to add the column to that content type. You need to add a new content type and add it in place of the old one as described here.
You also should be able to add it programmatically through C# (which can be translated to powershell) described here.
SPSite site = new SPSite("http://sharepoint");
SPWeb web = site.OpenWeb();
SPList lib = web.Lists["Your list goes here"];
SPFieldMultiLineText field =
(SPFieldMultiLineText)lib.Fields["Your RTF Column"]; // this is your site column
field.RichText = true;
EDIT: You can also add a list column and add that list column to the list instance of the content type, which would be much easier if your scope allows that.