I had another problem with the K3s in that it was unable to key the KPA500 using the AUX cable. I have had to use the RCA key line for a while. I could see no connection between the two issues but decided to investigate this problem as it could also have been related to KIO3B board.
The Keying problem turned out to be R9 on the KIO3B board which is simply a resistor in series with pin 10 of the AUX connector. As the Speaker IO problem was there with and without the AUX connector plugged in I see no reason this would affect the issue.
However on reassembling the radio the speaker USB IO was now present on the WSJT F2 menu. I have no idea what corrected the problem but it now works fine.
I had checked the LIN_SW circuitry while the KOI3B board was accessible and seen no problems.