There shouldn't be any conflict with Authorize.net at all. Providing you have the tracking code in place properly, it should all register just fine.

I use Authnet on the vast majority of sites I work with (Zen related) and they all record Google Analytics (including E-Commerce Tracking) just fine.

Maybe run a test transaction yourself to see if it records a sale. If you go through the process yourself you may be able to find out if there is a glitch in the process.

You would also be able to do a view source after you complete your transaction (on the thank you page) and be able to find out if the E-Commerce tracking is present and filled with data).