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Bottleneck in Data Transfer

Update:10-11Source: network consolidation
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We run a small network in our office consisting mainly of Intel iMacs we purchased several months ago. The server computer is a brand new Intel Mac Pro server with 4 500 gig drives raided together, two 2.66GHz dual core intel processors, all the other bells and whistles we could think of, etc. We added in two fiber-optic switches: one in the server room, one in the office. The switches connect to each other and the server with fiber optic cables, but the iMacs connect with ethernet cables.
We had the iMacs for a while but we just recently got the new server and upgraded our old 100 base switches. Afterwards we wanted to test out the data transfer speeds, as we plan to back up to the server frequently. We were dismayed to find that transfer rates capped out at 60 MegaBytes/sec according to the Activity Monitor's Network Activity tab. In fact, it would range mostly from 40-45MB/sec. None of us here have much experience with networking, but that seemed a tad too slow. My basic math tells me that a byte is 8 bits, and from that a Gigabit network should transfer data at 120 MegaBytes/sec, which is three times the speeds we were actually seeing.
We sent data both to and from the server in order to test this. Thinking it was perhaps a problem with the ethernet itself, we grabbed an external FireWire hard drive and transferred data from one of the iMacs directly to it and noticed exactly the same transfer rates. We plugged two iMacs directly into each other and transferred at the same rate, ~45MB/sec.
Well this was highly frustrating. All Macs supposedly ship with Gigabit ethernet since, what, 2002? Earlier? Why are our speeds so slow? We thought the hard drives might be slow, so we got info on the drives and googled them for their tech specs. The iMacs' Western Digital drives are capable of much much faster speeds according to everything we've read.
We started reading anything we could online that addressed this issue. Some information read the problem might be that the optical DVD-R/CD-R drive was only capable of slower transfer speeds. Since the optical drive and the hard drive are on the same bus it would slow down the hard drive's maximum transfer rate, much like having a Gigabit hub with a 10 base computer plugged into it would slow the entire network down (which is of course why we use switches instead of hubs). Is there any truth to this? If this is, in fact, the case, can we bypass this bottleneck somehow? I'm not talking about opening the computer and manually disabling the optical drive, as that's a waste of a perfectly good DVD-R/CD-R drive.
Also, if this is true, why in blue blazes is Apple flaunting Gigabit ethernet if the computer can only take advantage of 1/3 the speeds Gigabit ethernet has to offer?! I'll happily provide any more information that's relevant to the problem at hand.
Thank you
  Mac OS X (10.4.8)  

The Best Answer

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Here's the specs for the default Hard Drive that Apple put in here:
http://www.westerndigital.com/en/products/Products.asp?DriveID=137
From that page
Buffer To Host (Serial ATA) 300 MB/s (Max)
Buffer To Disk 748 Mbits/s (Max)
I have no idea what signaling overhead for my data transfer protocol means.
The ethernet cords are no longer than 20 feet, are all Cat5E, and are well shielded. There is little to no ElectroMagnetic interference in any area they run. The longest cable is the Fiber Optic one, which runs about... oh... 40 yards? These were all installed by professionals.
I feel it's important to stress the fact that we tested an isolated direct computer to computer transfer with a single 6 foot Cat5E Ethernet cable and still experienced the same speeds that we experienced over the network. We tested multiple computers, multiple cables, multiple files.