I've just started using Inkscape in Ubuntu 11.10 and I'm not sure what exactly triggers it, but at some point, the Inkscape viewport becomes unresponsive.
The viewport is still visible. I can still manipulate the window itself: move, resize, open menu items at top. The cursor switches style. But clicking on anything within the viewport has no effect.
I must close the file and restart in order to regain control.
The problem seems to be related to this bug report: https://bugs.launchpad.net/inkscape/+bug/785701, and the problem seems to be Inkscape trying to access files that are currently unavailable to it (files that may be on network shares or external disks that are currently umounted or disconnected).
Mark Roth's answer on that launchpad page had a good suggestion to run "strace inkscape" from the terminal in order to see what happens when Inkscape freezes. You may find that, rather than restarting the system, you can instead mount the disk with the file Inkscape is having trouble stat-ing then try starting up Inkscape again.
What hardware do you have? Your computer may not have sufficient hardware to run such an advanced resource-intensive program.