The CashRegister API is the only API that I have found that can query transactions *and* identintifies transactions by merchant issued order IDs. The latter is very important as it allows the merchant to track orders from the start. All other services (Authorize.net, Intellipay, Goemerchant, etc) track transactions by a transaction code issued by the gateway. The disadvantage is that when -for whatever reason- your site did not receive a response to the 'Auth' fase, manual intervention is required. You the merchant did not receive the transaction code and you can not query the service by your order ID.
This is interesting. I was playing around with a site that currently uses Authorize.net. When you "check out", they send you over to the Authorize.net gateway. Authorize.net generates a transaction ID for the customer and it passes that information back to the server after you fill out the credit card info. For the ecommerce package, I won't use this method of communication. The server will handle the communication with Authorize.net's gateway. Since a transaction ID is created before processing the credit card info, my guess is that there might be a way to grab the transaction ID for the direct connection method.
I'll call up Authorize.net to find out if I can grab a transaction ID from the server before asking the customer for the credit card number. If it is possible, then we can grab the transaction ID first and use that number to track the transaction. It won't be a merchant generated transaction ID, but it should work.
