I guess your only option for now is to disable it. I am really busy at work. I just can't find time to install 404SEF and figure out a solution. I can take a look at it when I get a chance. I'm sorry.
Anyone using 404SEF here, maybe you can help Baz.
Here's a little tip from me about SE0. I used to make my site URL pretty using SEF advanced. But I notice that no matter how pretty your URL is, it's not really going to boost your site ranking. What important is popularity and content. It's enough that you put the proper title and description.
Search "Joomla Components", "Joomla Modules", "Joomla Mambots", "Joomla Hacks" and so on... from Google. This site is in page 1 of google

. And i'm not using 404SEF or SEF Advanced! Examine the page on how I did it.