I have actually heard that even though every country, where you stayed longer than 6 months in a row, the CR is mandatory, CIC can still ask for CR from other countries you lived shorter time or if you spend multiple times in some country in a short period of time. So it might not be them being suspicious, if he spend there 2 rounds of working holidays visa, then them might wanna just make sure he's clear there. You say he has a clean CR, so you have nothing to worry about, it is just gonna take some time to get it.
When we were waiting for my husband's FBI PCC, I followed this thread and I found there a lot of useful information: http://www.canadavisa.com/canada-immigration-discussion-board/updated-topics/-t247817.2685.html;topicseen
Also, just some info:
- we took fingerprints at local RCMP (ink ones) and just one set - it was accepted by FBI
- it was exactly 12 weeks between the day FBI received it and when it was delivered to us
- according to some ppl in the above thread there is something to consider (but it's all pieces of info the collected from CJIS helpdesk agents: FBI puts your fingerprints through the scanner only weeks after they received it and after they charged your CC, so once they charge your CC, wait couple of days and call CJIS and ask them if your fingerprints were accepted. Their number is 304-625-5590 and they will be able to tell you estimation of when your CR will be dispatched and if your fingerprints were accepted, not what is the outcome of the search of course. If your fingerprints were not accepted, you will know right a away and you can start again instead of waiting for how many more weeks to get their rejection letter. According to the info they collected, some say you can send multiple fingerprints, some say they learned from FBI that they will just pick the best one and scan that one, throw all the others out without even trying. Anyways: go to specialized agency or RCMP, do not take the fingerprints yourself.
Also, take a pic of the application when it's ready to go, the courier slip and the delivery details, also the prinscreen of the waiting time for FBI background check on their website and communicate with CIC that it will take quite some time before you get this document.
Hope this helps, T