When you are adding a resolution code at the end of a chat session, please make sure that you are selecting the correct resolution code. One of the more confusing codes is the "Lost Call" code, which should only be used when a patron sends a question, never replies to your messages, AND did not login with an email address.
Julie Strange, the administrator of the statewide chat service in Maryland, AskUsNow!, has a nice chart detailing when to use each of the codes (PDF). (Please note that I'd recommend you never use the "Followup by Me" resolution code.)
Make sure that when you select a resolution code and click the "Add" button, you pause for about 5 seconds to ensure that the code is actually appended to the chat transcript. If you click "Add" and then rush to close the chat session, your code will not get assigned to the transcript, leaving it adrift somewhat in the system.