Actually how much new code has been applied to the 0.96-2ubuntu3 version?
There was absolutely no problem with the former 0.96-2ubuntu2 version as far as 
shutdown/rebooting issues are concerned.
This much has been publiced in launchpad about this update:

" debian/patches/04-autorestart.patch:
    - add autorestart support (LP: #499937)"

And then this is built to depend on two new packages:
- libdbus-glib-1-2 (>= 0.78)
- libgdk-pixbuf2.0-0 (>= 2.21.6)

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[Maverick] policykit is not responding
https://bugs.launchpad.net/bugs/623819
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