I disabled all the Firefox add-ons and the warnings continue. Unchecking the run Java option stops the warnings, but is impractical. I have seen other websites that suggest the use of Combofix - but this didn't seem to help.
I have saved all my Firefox Bookmarks and loaded them into Internet Explorer and am now using this as my default browser. Do you think that simply deleting Firefox and reinstalling it would get rid of the trojan, or is it hiding among files that will not be deleted?