The user was only using smart, neither apt, nor yum. See the following post

http://lists.atrpms.net/pipermail/atrpms-users/2006-October/006181.html
> Nope, I only have smart enabled. I don't even have apt or yum installed.

Furthermore the changes from a working setup and the broken one were
> [...] The only updates that I see that can have any impact are
> kernel (2.6.18) and libsepol. And for that last one, I don't have
> selinux enabled [...]