Hi,

Purely on personal experience (don't know if it applies universally) I think you are correct.

Our Australian site is site.com/order/ and has never had this problem. Our UK site is order.site.com and is the only site where we have noticed this occuring (i.e. sub-domain being treated as an entirely separate domain)

Google also ahs some good resources on this:

http://code.google.com/apis/analytics/docs/concepts/gaConceptsDomains.html

This also might be useful if you want to adjust the analytics code as opposed to the site structure

http://code.google.com/apis/analytics/docs/tracking/gaTrackingSite.html#domainSubDomains

Dylan

First touch tracking might assist in getting clearer analytics. We tested it in a similar situation and it did make things much clearer. Note that it isn't necessarily tracking the immediate referrer to the store or order page - but the first one.

Seomoz itself has a really good blog roundup on the process

http://www.seomoz.org/blog/first-touch-tracking-in-google-analytics

Cheers

Dylan