Hi Lisa,

Sorry for our delay in replying - we're all out of the lab at the moment after OHBM. I will return next week and will be able to deal with your question in more detail then.
I am not surprised that there are some differences between the results produced by the two programs but I can't say for sure what exactly the source of the differences is until I have a look at some data myself. Your commands look reasonable to me.
You're right about using polort 0 as linear and quadratic trends are removed during preprocessing.
Rather than looking at the residuals, I would have a look at some correlation maps generated using the two different residuals files - are these notably different?

I will try to get back to you as soon as I can!

Clare