Hi Veronica,
When the state machine first connects to the Bpod application, it sends a request for any connected modules to return a self-description. Normally, when modules are idle, they continuously check their port for incoming commands - but if the module is (for whatever reason) in the middle of an operation (e.g. if it is stuck waiting for bytes to arrive over USB), it may not return a self-description. Module ports that do not return a description are automatically named 'SerialN' where N is the module index.
In cases where you're seeing 'Serial1', what was the rig doing just before (i.e. was there a crash? Or did the previous protocol end normally?)
If you press the 'Module refresh' button on the Bpod console, does it return to the correct module name?
-Josh