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I registered to both sites, thinking that sadly they'd be independant... but one the first, they game me the nick sitename-20 and on the second sitename-21. So i assume that's been done at a global level?
Is there a way of getting payed as one? I take it amazon can't refer a viewer to the national amazon (if it exists).
Surely it would be in their interest to do so.
Please remember the Amazon.co.uk Associate Programme is completely independent from the Amazon.com Programme, so when you join the Amazon.co.uk programme you do not automatically become an Amazon.com Associate as well. You will only earn referral fees from links you set up to the Amazon.co.uk site, not from any links you set up to Amazon.com.
So it would seem they are separate entities. They probably use some of the same backend for tracking, which may be why you got such a similar affiliate code.
You could setup a script as Mack suggested, or offer 2 links, 1 for each destination.