Please keep in mind that the usage of the multiple processors or multiple cores, is determined by the operating system, in this case by Microsoft* Windows* Server 2008.
So it is possible that the operating system is assigning only one core to run a particular task or software.
I would suggest contacting Microsoft* and asking them if when you run multiple copies of the same software, will the operating system assign one copy to each processor or core, or will it assign al copies of the same program to the same processor or core?
I would suggest installing all the available updates for your operating system as well as for the running applications.
Also make sure that you have the latest BIOS version for your server board.