Answer
First check for available Developer Studio updates via the Help menu, since this kind of inconsistency between the two similar actions has sometimes been an already-fixed tooling bug in an older build. If updating doesn't resolve it, clear Developer Studio's Cache Directory (found under your user profile's AppData\Roaming\DeveloperStudio\<version>\var\cache folder) and try generating code again — a stale or corrupted local cache is a common cause of this specific discrepancy between the standalone Generate Code action and the combined Generate Code and Deploy action.