What I think about non-issuance of MR is this, they might be having challenges with those ones in terms of meeting the points for PER. Agreed that you or the person concerned got PER which is usually from the Central Intake Office in NOVA SCOTIA, AVO will re-confirm to ensure that the person truly meets the needed mark. They will match documents with claims and all of that. They might even have spotted some inconsistencies in the application that was not spotted by CIO or are carrying out further background checks on that file before they determine whether to issue out MR or not. Remember, this is under probability and I am basing my comments on antecedents. Some of the people in my set (FSWP 2013) where affected by what I just stated. Also, some people might have informed AVO of status change. This can cause delays in issuing MR.
Be as it may, I am not restricting my comments on just quotas but I believe that it is a huge factor. There is also the likely concern over prioritization. They(AVO) might have decided to suspend temporarily working on FSWP 2014 category and even EE to concentrate on other PR schemes (Asylum seekers-refugees, Parent scheme - Super VISA, etc) . They will definitely return to it later. Again, quota might be affected here. They have certain number of visas that they cannot issue out for a year. Globally, it is usually from 250,000 to 270, 000 plus visas. Check the links that I have sent. Let us say that AVO already had the visas to give out for year 2014/2015 for FSWP 2014 and then comes EE which only started early last year (January, 2015). Then comes the concern of the Syrians which will cut across all VOs (even those that were initially fast before now have slowed down pace). This I strongly believe is a concern.
Again, from the little that I know, their visa quota year runs from MAY TO APRIL. If EE started in January of 2015 and they promised speedy processing of their applications, that will affect already submitted applications (FSWP 2014, Asylum seekers etc). This is part of what I am basing my points.
I have given my opinion about backlogs that were returned that you mentioned. Those applications were not even processed. Nothing like PER or NER. Some had applications with them for over 3 to 5 years. Rules kept changing and they had loads of applications. They felt that it was the best way possible to eradicate the backlogs and then start a new fast tracked program. My set (FSWP 2013) was the first beneficiary of it. Yours should have naturally followed but I believe some if not all of the highlighted reasons are why we have the unusual scenario. Your applications cannot be returned. MY REASON : THEY HAVE PROCESSED A LARGE CHUNK OF IT. If they had not been processed, returns and refunds would have been a good guess. I do not see it happening.