I have now had the chance to sort out the data from last night's test and produce comparison graphs of wattage against time for the PowerTap and the CompuTrainer during my FTP test. As you can see from the graphs below the units tracked each other very closely, certainly not a large enough difference to be significant especially when the vast variations in day-to-day athletic performances which can't readily be explained are taken into consideration.
From the data I calculated my best 5 minute and 20 minute powers and from the 20 minute power my estimated FTP, the results are shown below:
MP5 - 357W
MP20 - 310W
FTP - 294.5W
MP5 - 361W
MP20 - 312W
FTP - 296.4W
So, if the FTP is the pearl I am looking for the difference between the 2 values is 1.9W, or 0.64%, that's accurate enough for me!