That's a known behavior of WTP Server adapter. After eclipse is started all modules added to the server have the same publishing state. This state is called PUBLISH_STATE_UNKNOWN. When deployment starts first time through context menu for server instance in servers view or as an auto publish it always starts as inceremental publish, but during processing this regquest it analize modules states and if it foung module with PUBLISH_STATE_UNKNOWN it changes incremental publish to full publish.
That happens because WTP Server Adapter doesn't save deployment state between sessions,