Hi Carl,
Are you using the same information in your feeds that are being sent to Google, Amazon, and Ebay? If not, that could be a reason your Amazon & Ebay listings are outranking your primary site’s listings.
If you are sending the same information, the reason may be because you need to increase your product bids. Products in a very competitive category with low bids will have a very hard time gaining exposure because they’re ranked so low. Try increasing your product bids until you start seeing your primary site’s listings outrank the Amazon & Ebay listings or rank beside them in the SERPs.
Regarding your second question, you actually don’t want to remove any listings from the Amazon and Ebay store fronts. Removing the listings will only decrease the amount of coverage you’ll receive on the SERPs and lower your traffic. If you keep the listings on Amazon & Ebay, you’ll have three times the coverage (the Amazon listing, Ebay listing, and your primary site’s listing). Yes, you’ll be paying Amazon and Ebay the costs associated with those clicks, but you’ll still have an ROI that’s better than no ROI at all.
Also, your account could be under a random review. We’ve been seeing this happen to various accounts in the past few weeks. You can read more about it here.
Hope this clarifies some things!