Hi Aldus,
I know that this is quite an old question, but as I had the same problem I just want to add my findings to clarify it a little bit more.
The difference between the ports Workstation 1 and Workstation 2 is the different interpretation of midi commands received on these ports by the Tyros2.
The kind of interpretation can be configured in the keyboard for each midi channel on each port individually.
This is described in chapter "MIDI Receive Settings" on page 216 of the "Tyros2 Owners Manual".
The following is based on my Tyros2, but it should be similar on your instrument.
If you go to the RECEIVE page in the midi settings of the Tyros2 you see the following:
The "digital keyboard-1" is internally called "Port 1" and is configured to "SONG" in the PART column for all midi channels by default. This means that the midi data is just used for creating sound, which is what is needed when the Tyros2 should behave as a plain sound generator, e.g. to play a midi file using an external player on the PC.
The "digital keyboard-2" is configured differently by default. The PART column shows values like KEYBOARD, EXTRA PART and others.
E.g. KEYBOARD means that the received midi note is interpreted as a key has been pressed on the keyboard. As the voice currently assigned to the keyboard may be different than the voice used in the midi file, the result sounds different. This effect was the reason why I discovered this problem.
Unfortunately you can not configure "Port 2" to work equal to "Port 1", means that you can not assign "SONG" to the channels of "Port 2". May be the reason is limitations of the instrument.
Hope this helps,
Peter