Hmmm... Good point.
At the moment, the counting of inserts/updates is done at the "logical" table level, rather than the lower physical table level, in order to make it simpler. The logical level does not actually know if an update was cancelled because there was nothing to do. We'll have to address this.
There is also an "IO Logging" capability, which records the actual SQL issued at the physical level. Turn this on (Tools - Start IO Logging). You should see the second update substantially reduced or disappear.
NOTE: The IO Logging currently only works for SQL based targets such as CRM and SLX.
Regards
David