We don't have a lot of experience using the output from the Viking ECU. We don't generally have this issue with other ignition systems, so I don't know if it's just an issue with your install or the ECU in general.
1) Do other Viking users have any issues when hooked to EFIS systems? It could be that the output of the ECU does just vary.
2) Are you sure the prop is not actually changing speed?
3) You can try pin 34 on the EMS. You won't hurt this pin with the output from an ECU, but it might not work at all. Might fix it too.