If both of your Macs have Gigabit Ethernet, and I assume that your have an AirPort Extreme Base Station (AEBS) that also has Gigabit Ethernet ports, it really doesn't matter that one of the Ethernet drop cables that you are using is not rated CAT-5e. CAT-5 will work.
Were you attempting to transfer files between each of the Mac's internal HDDs, via the AirPort? What are you using to measure the data transfer rate? What rate do you get if you manually set both Macs for 1000baseT full-duplex?
* Correct, AEBS with gigabit
* I am using a simple copy paste between 2 Finder windows. I am transferring between the two internal HDDs via the AEBS
* I am using Traffic Monitor which came with Intego Virus Barrier. It is giving consistent numbers with the iStat Pro widget
* I had not been able to get the MacBook Pro (model5,5) to connect at gigabit but based on your comments I swapped out the CAT5 cable on the MacBook Pro (model 5,5) with a new CAT5 cable I had lying around and now get a gigabit connnection - so I guess there was something wrong with the old cable???
* Now I've restarted the file transfer. In the first 30 seconds or so the speed gets up to 40MB/sec or more but it fluctuates wildly and eventually settles down to apprx 300kb/sec. I can see that the "out" speed on the Mac Pro is showing the same reading as the "in" speed on the MacBook
Just one other thing I also tried using the second ethernet connection on the Mac Pro in case there was a problem with the card but get the same results.
One more observation
The file transfer dialogue indicated over 1 day to transfer a 105GB file! (based on a ~300KB/sec network speed). I went for a coffee and came back 2 hours later to find that it had finished so did the transfer speed up once I had left or are the speedometers I was using incorrect?