Aha oh you fixed it? Good to hear! Yes I had a fairly similar quarrel once, can't remember the details but I discovered that sh404SEF can force my Joomla site to strip the www. on every DNS request (or whatever) - Daniel only just recently did this to Compojoom and it does indeed save headaches and give you brownie points in the SEO department (apparently).
...well now that was my kind of bugfixing... Cheers Mike!
EDIT: And you wrote that reply as I was writing this reply
Out of curiosity, how do you strip the www. usually? I'm pretty sure I do it through an sh404SEF option but it looks like you use a different SEF extension.