MBP 2.6 ghz slower than dual 2.0

Hi people.
I traded my dual 2.0 g5 for a 2.6 ghz mbp. I needed a portable solution and could not afford two computers so this was the solution. I put an esata card with two drives and the data rates with this solution are the same as in the g5 (80mbps per drive), so far so good.
The problem is that running the same software versions for everything, the mbp is more than twice slower. For example a 90 min encode in compressor (custom one pass fixed rate) is about 4 hours in the notebook, and about realtime in the g5.
I have 2gb ram in this machine and had 1 in the g5. System is snow leopard and final cut studio 2.
Any suggestion before I have to clean install everything?
As always, thanks a lot.
Pepo

Custom installation on a factory new machine won't give you many options other than leaving out iLife, a bunch of printer drivers and fonts. That should not affect FCS performance, even the most basic Intel CPU based Mac should be faster than a G5.
Have you run Software Update, repaired permissions on the boot drive, etc?

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