That's very odd... I never considered the CIC officers to be capricious like that... Usually if the math works, and the 1095 days are in compliance and there aren't too many exits, everything is smooth.
I am self employed (independant consultant) with customers all over the world and I use Nexus to travel in/out of Canada. Nexus is based on iris scan and therefore no stamps were posted in my passport.
The CIC officer couldn't match my trips to passport stamps and therefore gave me the RQ.
The absurd is that they told me they can't pull out a list of entries/exits to/from Canada from the border control (i.e., immigration).
So immigration, isn't communicating with immigration
But this was expected, and I understand their need to look into this further.