change VPSCONFDIR:=/etc/vz --> VPSCONFDIR:=/etc/vz/conf
then start VPS machine (ONBOOT="yes") with /etc/init.d/vz start
The proper new location for $VEID.conf files is /etc/vz/conf. If vzctl is upgraded and the previous version is less than 3.0.10 the appropriate warning is issued -- you have to move $VEID.conf files to conf subdir manually.
I just commited the necessary changes. Hopefully this fixes the issue. If not, please reopen the bug!