Go back to the Urchin tracker, Allan.
I realised that the GA tracker was not picking up every Ecommerce transaction and asked the Google team to help as I couldn't find any issue after modding the file to comply exactly with Google's help information.
After extensively testing everything and being nailed by me on what their help files say they admitted that the GA tracker "in extremely rare cases"

does not track Ecommerce and goals correctly and that they are working on solving this issue. I was told to go back to the Urchin tracker until the issues are solved.
So not everything can be blamed on the tracking module
Cheers,
Edward