I had exactly the same thing with three different debian and ubuntu containers. It turned out that they were all using older versions of the apache2.2-common package than was on the new server.

If you cat any of the suspect files from outside the container, the contents are just a pointer to the location of the missing files:

cat /vz/private/137/fs/root/etc/apache2/ports.conf

gave something like:

//ubuntu/9.04/x86/apache2.2-common_2.2.11-2ubuntu2.2_i386/etc/apache2/ports.conf

The package was missing from /vz/template/ubuntu/9.04/x86 on the new server (somehow the migration process had not copied it across). Rsyncing the correct directory from the old server to the new and restarting the VPS fixed the problem on all the problem containers. In the case above I ran the following command on the old server:

rsync -avz -e “ssh -l root” /vz/template/ubuntu/9.04/x86/apache2.2-common_2.2.11-2ubuntu2.2_i386/ 172.16.1.1:/vz/template/ubuntu/9.04/x86/apache2.2-common_2.2.11-2ubuntu2.2_i386

to copy the required files to the new server.

Cheers,