The only thing I can suggest re: Mewig is that if you go from 'Files' to 'Sound Settings' by clicking on the 'Sound Settings' tab, the options are
always greyed out. You have to click the 'next' button, (if you're converting from DVD you'll notice the DVD drive reading the information on your disc at this point). I have no idea as to why it can't read your mplayer/mencoder files anymore.
The only other applications I've used for conversion are
Cowon Jet Audio (you have to set the conversion to the Cowon D2 profile), and
Virtualdub. Virtualdub is great (and a small download), but it takes a bit of fiddling to get the X20 profile right.
My Iriver Plus 3 did the same updating process, and now every time I start it up it downloads 'basswma.dll' all over again. I hardly ever use this software, though.
Hope this was of some help.