As a followup, we got some help from Nino and Rotax, who viewed the log files and immediately found the problem--SBE--Stupid Build Error. On the RV-12iS (with 912iS engine), we have to disconnect two of the Crankshaft Position Sensors (CPS) in order to properly attach in engine mount. We swapped the two connectors when reconnecting, with the strange and unnatural behavior we observed as a result. Swapping the connectors to their correct positions worked wonders.
Thanks to all for their advise.
Rob