I started advertising on Google shopping this week and it's going great, apart from the traffic/sales are getting attributed against google/organic in Google Analytics.
The conversion data tracks correctly within Adwords, and if I run a normal AdWords campaign (keyword based) this traffic and attribution shows against CPC.
The Google Analytics and Merchant Centre account are both linked.
Setup the autolink between AdWords and Analytics. This is done in the admin section of your analytics profile. With this link, by default AdWords will autotag all clicks. You'll get all the data you want in the AdWords section of Analytics.
Do you have auto-tagging enabled in adwords?
When you are logged into adwords click on the gear in the upper right and go to account settings.
How are your feeds setup? Your feed software could be appending the incorrect UTM parameters to the destination URLs. View the product list report in Merchant Center to see the submitted URLs for a sample of products that are showing as organic traffic in analytics. I've never heard of this happening, so something is stuffed up along the setup process.