We fixed this issue and it will be included in the new release.
There are couple things to note. First, you should add the following to the HEAD section of your modal dialog page:
<base target=_self>
Otherwise, the page opens another window when submitted.
The second thing to note is that even though the new JavaScript file will let your page retain the editor HTML value after the postback, there might be some other UltimateEditor functionality which might not work properly because of the nature of the modal windows. They do not work the same way the windows opened as regular (non-modal) windows. One common problem is that the modal windows are cached and this behavior might cause unexpected behavior.