Ok, i'm confused. I have my machine it was running a P4 650 (3.4Ghz OC to 3.9Ghz), I have now put in a Q6600 (2.4Ghz OC to 3.4Ghz). My times used to say 2:10 for all the wu in my queue, now and only after doing a run benchmarks they all say 3:20! but my benchmarks are faster than they were on my P4, A lot faster.

Can anyone shed some light on whats going on here?

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Sure, the RDCF(result duration correction factor, in Boinc) for the new host hasn't adjusted itself yet, whereas the old machine has done enough wus for it to adjust. Run 20-30 or so wus on the Quad and it too, will adjust downward to reflect more realistic values. The estimated time uses Fpops est (supplied by Rosetta with each wu), Benchmark score, and RDCF to guestimate how long it will take. The RDCF will adjust as wus are returned and should be going down with each return. If however, it takes longer than estimated, the rdcf will adjust it upwards in one step.

Though it should be noted Rosetta@Home will not crunch any shorter or longer than the ~3hrs

The way R@H works is you specify how long to crunch for and it tries to do as many complete calculations as it can in that time.
By default it is set to 3hrs, your old computer may never (on average) have been able to do work for the full 3hrs and hence you ended up with 2hr 10mins as the average run length. You may find that since the Quad can get the same amount of work done in a lot shorted time on a single core then your time ends up much closer to 3hrs (since it can slot a few more complete calculations in)

you could if you wanted alter the run-length in you preferences (under R@H preferences) to suite your particular computer usage.
If you leave it on all day, then set it to 24hrs, save you some bandwidth and r@H some bandwidth.

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