Running Inkscape 0.48.2 r9819 on Ubuntu, the program seems to eat away any custom xmlns I add to the svg tag.
I've tried both editing one into the file with emacs, and using Inkscape's XML editor to add the property, then saving, closing, reopening.

Has anyone encountered this? Is there a preference or something less obvious to tweak to prevent this?

Cheers,
//ata

Sounds like the issue described in these threads: viewtopic.php?f=16&t=10763, viewtopic.php?f=22&t=1055, viewtopic.php?f=16&t=11243

Thanks. The second topic is close - an API and UI for adding custom namespaces would be the next question.

I found the relevant bug on launchpad: https://bugs.launchpad.net/inkscape/+bug/166004

So, for my particular purposes, as long as I'm happy to edit the xmlns in by hand, I just need to be sure to add an actual dummy tag using that namespace.
Previously I'd only added namespace specific parameters to identify objects by (relying on id gets tricky sometimes).