The situation is very odd on my end.Did you implement the code in your site? Have you tested in your other target stores? I have UK, US and CA and tested with VPN IP's for each location to see what I got when a user followed an affiliate link.
Also, test out the shortened amazon url to make sure it is converting. I found that if I used the shortened link it did not capture the cross store traffic, so went back to using full links. Do some testing on that to ensure you are being credited with the click through.