Yes.. u are right ..they don't consider reference letters from colleagues as a conclusive proof, especially for NOC 1122..had it been some other NOC, they might have considered it..their process is pretty wayward..while filing the application most of us followed CIC & VO checklist. But post July 18, a new checklist(general) was introduced ..and i believe they are following that, which is unfair in case like u since the new checklist doesn't mention abt providing explanation letter(or colleagues ref) in lieu of supervisor/manager ref letter.
You can appeal ur case, as i think u got NER not for irrelevant job duties, but for not providing work documentation as per new checklist..
Below link will best guide u..
http://get2canada.wordpress.com/how-to-deal-with-unfair-ner/