The issue was brought up about two weeks ago and it seems like Google is well aware of it. However, a solution to the problem is still nowhere in sight even though the company has promised to take care of it in a timely manner. What is causing all the troubles is not exactly clear just now, but it looks like Google Checkout is not processing all orders correctly resulting in a number of downloads being marked as shipped, yet the respective developer account does not get credited for that. Nevertheless, it has been confirmed that all developers who got underpaid will have their account balances fixed and will get reimbursed for the missing amount of money.
source: Android Market Forums via Electronista