Mac Pro 2.0 outperforming Mac Pro 2.66, WHY?

Ok Guys, I am stumped here and hopefully someone can shed some light.
I have 2 Mac Pros: System 1 - 2 x 2.66 with 9GB of memory and System 2 - a recently acquired 2 x 2.0 with 5 GB of memory.
System 1 has banks filled as follows:
Riser A
Bank 1: 2gb
Bank 2: 2Gb
Bank 3: 512
Bank 4: 512
Riser B
Bank 1: 2gb
Bank 2: 2Gb
Bank 3: empty
Bank 4: empty
In System 2, I installed snow leopard after reformatting a 500 GB WD (7200rpm)caviar drive w/16 MB cache. There is also a 2nd WD drive (1 TB, 7200 Rpm)
Having plans to upgrade the 2.O Mac pro, I decided to compare it against my "faster" Mac pro 2.66. I took a video file that is 1hr 23 mins. It took 56 mins to render in IDVD coming from ImovieHD. Knowing that the 2.66 is significantly faster than the 2.0, I was thinking it would take maybe 44 mins to complete on the Mac Pro 2.66... to my surprise it took 1 hr 49 mins.
Thinking that the benefits were due to snow leopard. I backed up the system, reformatted the drive and installed Snow leopard and all my apps on the Mac Pro 2.66. I did the same test, the performance was even worst - it took 2 hrs 3 mins. After dropping the F-bomb a couple times I started looking at other things.
The Mac Pro 2.6 has 2 x 1 TB 7200 drives the OS drive has a 32 GB cache the other drive a 16 Mb cache.
The memory in the 2.0 is configured as follows:
Riser A
Bank 1: 1gb
Bank 2: 1Gb
Bank 3: 512
Bank 4: 512
Riser B
Bank 1: 512
Bank 2: 512
Bank 3: 512
Bank 4: 512
The video files on both systems are located on the non-OS file but I create the disk image from IDVD to the desktop on the OS Volume. The workflow is identical on both systems.
Both video cards are the stock Nvidia 7300. All drives are 7200 rpm. Why is my Mac Pro 2.0 outperforming the MacPro 2.66 with almost twice as much memory? I even filled the two empty slots on the MAC pro 2.66 thinking that is why it was taking a hit, it did not help.
Any good suggestions welcome.

Some tidbits:
RAM should be in quad and paired across Risers.
4 x 2GB (or 4 x 4GB) is your best as far as memory bandwidth
6 DIMMs is not ideal (8 DIMMs properly paired is okay but higher latencies)
Higher density RAM also shows improvements.
HARD DRIVES are an easy investment and can be used in whatever system you need now or later.
7.2k drives are fine, yours are on the old side.
Especially that 500GB model.
SATA III, latest models, show 20% improvement, 64MB cache
4 WD Caviar Black 640GB @ $70 eachm or 1TB to 2TB ($85-170)
boot from one, and stripe the other two or three.
You probably aren't ready to throw SSDs in, nor do you want $200-275 for 10K WD VelociRaptors (300-600GB) which are fast and make nice drives for system, scratch, and of course in arrays.
Other throught - cpu upgrade project 5300: get a set of 5355s off ebay and have an 8-core frenzy for $400 the set.
2006 Mac Pro Clovertown (Quad core) CPU Swaps Revisited
2006 Mac Pro Quad-Core CPU Upgrade report (5350's OC'd to 3.3GHz)
http://www.youtube.com/watch?v=xOF435jCg8E
http://www.xlr8yourmac.com/archives/jan11/011311.html#S28002
- search cpu upgrades
http://www.xlr8yourmac.com/cpucards.html
Time to replace those 7300s, if they aren't ready to bulge and blow a capacitor already. Shame that there really are few choices, 5770 or... 5770.
OS drive should be lean, fast, and just OS and apps
data or media drive
editing drives
higher capacity drives w/ 64MB cache are a plus, just being 3rd generation of Caviar Black line improvements rather than 4 yr old 500GB 16MB cache model
+Tried to break-down and decipher your setup and results for my own use:+
System 2
Installed snow leopard
500 GB WD (7200rpm)caviar drive w/16 MB cache.
2nd WD drive (1 TB, 7200 Rpm)
Mac pro 2.O against my "faster" Mac pro 2.66.
video file is 1hr 23 mins. It took 56 mins to render in iDVD coming from ImovieHD.
I was thinking it would take maybe 44 mins to complete on the Mac Pro 2.66... to my surprise it took 1 hr 49 mins.
Thinking that the benefits were due to snow leopard. I backed up the system, reformatted the drive and installed Snow leopard and all my apps on the Mac Pro 2.66.
I work with a 2006 2.0 and a 2009 4-core 2.66GHz and the difference between the two is noticeable enough to consider upgrading my 1,1 to 5355s, 4 x 2GB (or more), and 5770, JUST so it can 'compete' on equal footing with $2k Mac Pro Special:
http://store.apple.com/us/browse/home/specialdeals/mac/mac_pro
Or for just $1800
http://macperformanceguide.com/blog/2011/20110123_MacProBargain--macpro.html

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jvknowles wrote:
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