My PR application got rejected when I applied through FSW program. I have an IEC work permit and a permanent full time job here, and I called CIC twice to check am I eligible to apply for PR through FSW AEO with IEC work permit and both times they said yes. Last year around Christmas I gathered all of my papers and sent my FSW AEO application. They returned it in February because I forgot to sign CC form and I've chosen wrong visa office (instead of selecting CPP Ottawa I've selected visa office responsible for my country). I also received detailed letter explaining what was wrong with application and there wasn't anything related to my work permit being not eligible for FSW AEO program. I corrected mistakes and sent my application again. Somewhere around beginning of April my CC was charged and on 11th I received email from CIC stating that my application for PR through FSW AEO program was rejected because of the type of the work permit I hold
So, I lost some 4 months in shuffling papers with CIC and some two months in waiting to take English exam again because my IELTS score was too low for NOC level A and CEC. And after all this, everything I hear for CIC service over phone is taken with a grain of salt and double checked. At the end, I'm still certain that the person who decided to reject me was wrong but I didn't have time to go lawyer and through appeal process (if that even exists).
Basically, when you send your PR application, one person checks all of your papers and if everything is OK they will charge your credit card or cash in certified check, if everything is not ok, they will send application back to you. And then someone will again check all of your papers and decide to issue you an AOR or not.