Thanks to Robert O'Callahan for providing an easy workaround, now I can start testing WriteArea in Firefox 3.1. All that was needed was a background-color:#FFF for the <html> and now it's working again :-)
Of course, using FCKeditor 2.6.1 is boring, so I've updated to the current SVN, and now some of the modifications aren't even needed anymore because the problem has been fixed directly in the FCKeditor main line. Anyway, working with SVN makes very easy the upgrade process and I had a script ready so it takes care of the packaging and removal of unnecessary files in order to re-package it as an extension for Firefox.
So very soon a new version will be ready, just some testing that nothing is too broken and I'll release it.
PD: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2a1pre) Gecko/20081211 Minefield/3.2a1pre