I'd say this issue is also related to outdated software in scorpio server. They are running php 5.2.13 (latest 5.2.16) and probably some outdated 2.2.x apache (latest 2.2.17).
Kernel is old too. 2.6.18-164.15.1.el5.028stab068.9 #1 SMP Tue Mar 30 18:07:38 MSD 2010 i686
Latest stable from kernel.org: 2.6.36.2 - 2010-12-09
-.-
Ouch, that's old OpenVZ kernel. There is already a localroot exploit out for that version. No wonder how you got rooted, it was only a matter of time.