8.4 to 9.2 migration performance

I am migrating a Postgres 8.4 installation on a dedicated server to Postgres 9.2 running on a Virtual Machine. A sample query that run in 10 minutes on the 8.4 installation take 40 minutes on the 9.2 installation.

Current Server, Postgres 8.4

* 6-core, 3GHz AMD system

* 12GB of RAM

* 4 SATA drive RAID-1 storage

* Mandriva OS

* SQL encoding and 'C' collation

Virtual Machine, Postgres 9.2 ( two different systems)

* 4-core, 3Ghz Intel system

* 12GB or RAM

* SAS storage on one, and 4-SATA drive RAID-10 system on second

* CentOS 6.3 OS

* UTF-8 encoding, and I have tried both 'C' and en_US collation

The first VM is at a local Data Center and the second in on a dedicated server in my office. Both give similar results.
The data, indexes and constraints have all been successfully migrated to the new system.
I have tuned the VM systems using pgtune with no significant before and after difference.
The 'explain' output for the query is very different between the two systems.

It seems like I am missing some simple step for there to be such a huge performance difference.

Any suggestions on what else to text/check would be very much appreciated.

Tom