If your E-junkie Seller Admin > View/Download Transaction Log does not show those payments, that means that Google Checkout has not informed our system that those payments were completed, so you'll need to investigate why.
If the payments show a Completed status in your Google Checkout account, then double-check that your API Callback URL and Method are correct:
http://www.e-junkie.com/ej/google-checkout-shopping-cart.htm
If the payments' status is not Completed in your account at Google's end, you will need to figure out why or what you need to do to complete payments, for which you should consult Google Checkout help page or support staff for any assistance you require:
http://checkout.google.com/support/sell/bin/request.py
Your Google Checkout account should be configured to complete all payments automatically. If you have enabled Shipping/Buyer's Address in your E-junkie product settings, Google may require you to manually mark each order as Shipped, and enabling Shipping would also add a 15 min. delay after checkout, during which period Google allows the buyer to cancel their order before they would notify us of completed payment so we could issue any download links.