Due to an offset in signal handling with the new firmware, the primary and secondary trigger events CAN come too close to each other. Not saying this is what happens here, but very likely.
This means that the secondary trigger event comes just before or just after a primary trigger event. When that happens the tooth count is wrong and the error is flagged, one cam rotation and 23 teeth passes by, the other 25, some 24... wrong. There should always be 24 teeth between each secondary trigger event.
Try setting the secondary trigger edge to be falling, instead of rising.
You can change the primary trigger edge instead, don't touch the secondary. But then you'd have to strobe the ignition and adjust "TDC after the trigger", on the other hand that is what you should do anyway!!
This is very obvious in a triggerlog, I can't see why making one doesn't work for you. Which VemsTune release have you tested it with?