What the agent said can't be true for one simple reason: the CIC letter mentions specifically that you have 30 days to take all the steps stipulated therein. If it took CIC 6 weeks to hand over your case to the local VO you would run out of time even before you would have the opportunity to submit your passport and photos.
In fact, I wrote to the local Canadian embassy, which has been a lot more helpful and prompt whenever I had an inquiry than CIC itself, and they told me to submit the passports right away, as accompanied by the photos and height/eye color info, to the nearest Canadian Visa Application Center (CVAC). Then, the documents are sent to the Visa and Immigration Section with the Embassy, which will do the rest.