If your Project is exactly the same (no effects added) and the Export settings are exactly the same (lot of settings to check and verify, but I would take the time to note everything in each program's Export settings), the times should be much closer, than what you indicate.
Some have indicated that CS3 is a tad bit slower, than PrPro 2.0, but not to the extent that you observe.
You might also find Bill Gehrke's Benchmark site and also the benchmarking spreadsheet and utilities to be of use. If nothing else, it will let you know where your machine fits into the others' machines. It can also help one spot bottlenecks, though your observations seem to be about 2 flavors of Pr and the same machine, Project and Export settings.
Is your P6 install maybe linked to an accellerator card? (such as Matrox or Pinnacle card?)
The video was a film. After cropping it was 1 hour 27 minute long. No effects, nothing at all added. When I saw how long it took to export [in CS3] I later exported exactly the same through Premiere 6 and it took 43 minutes.
I do have a Pinnacle card but it is only linked to Premiere 6. I use it to import. I woul prefer to use Premiere 6 for any work that I do but the programme has a fault. As soon as I put anything into the timeline then 6 crashes. I have reinstalled on numerous ocassions and it will work fine a couple of times then crash again. This is the only reason that I have CS3.
I forgot to add that Premiere 6 and CS3 are both on the same machine.