From what was described in your first post above, that affiliate problem was happening because your CB affiliates joined your affiliate program for one CB account, but you were using a different CB account for checkout, so CB's checkout site did not recognize those affiliate referrals has having anything to do with the CB account that was receiving the checkout payment.
To fix this, you simply need to go into your E-junkie Seller Admin and click Edit Profile, make sure your ClickBank Vendor ID matches the CB account that your affiliates have joined. It's probably also a good idea to change your Secret Key in that CB account and in your E-junkie Profile, to make sure they match exactly.
It may help to understand how CB affiliate referrals actually work. Clicking a CB affiliate link sets a referral cookie in the buyer's browser and then redirects the buyer to your sales page. Setting a cookie works basically like giving the buyer a "ticket stub" as proof of their affiliate referral, so they can show that "stub" to CB's checkout site later. When the buyer proceeds to checkout with CB, their checkout site looks for that affiliate-referral cookie stored in the buyer's browser. If it finds the cookie, it compares the CB account running that affiliate program with the CB account receiving the checkout payment. If they're the same CB account, they will credit the referring affiliate for a commission; if they're not the same CB account, or if there's no referral cookie detected at all, no commission is granted.