The Method of Payment (Check, Cash, etc.) is based on a user defined list.
Click Tools > Custom List Setup > Payment Methods to ensure that you payment methods are set up properly.
There are payment Method Types. Each Method can be in one of these Method Types. The Types are Check, Credit, Cash, Stock, In Kind and Other. For example, you can create methods for Visa, MC, Disc under the Credit type and Securities, Stocks, Bonds under the Stocks type. Users in the UK or Canada can create a "Cheque" method under the Check type and so on.
When running a Transaction Report, you can filter based on a Method Type or a specific Method. Click the Methods tab on the Transaction Reports screen for this option.