Hi,
I tested an upgrade from 3.4.0 to 3.4.1 on a fresh install of Sid and it doesn't report any issue.
What is the output of "ls -al /var/lib/tuptime"?Did you reboot the computer between the 3.4.0 installation and the upgrade?
Please, can you add here the output of 'su -s /bin/sh tuptime -c "tuptime -x"'?
Thanks,