Medicals - this one you can see from application. (also sometimes they do review it and even pass it preliminary, but they are waiting for something else - mostly additional PCC request or forwarding one that had long leadtime on your side (because they have additional Canada checks for inlanders, that is why it takes so long to pass in most cases). It can be done somewhere between 1 week to 1 month after medical results are uploaded by your doctor.
Rejections here are rather low and in many times they can be appealed (most people are aware of their health). It is more common to get ADR for more medical tests at this stage (which will slow down process but nothing else).
Criminal pass - they pass them usually at the day when they also pass your medicals (common practice for outland applicants).
At this stage rejections are most frequent (according to statistics people have problem to send correct PCC, send it at all or send evidence why it takes so long, or ask for official application from CIC directly for their PCC)
R10 - they do the first check around the time when medicals are passed. They also start your security checks around that time. But they will only finish them once they have all needed documents there. So some people get ADR asking IELTS or TEF or ECA certificates (after medical passed for outlanders and within 1 month for inlanders). They also wait for PNP confirmation from your province (for all PNP). This part can take anywhere between 1 week and 2 months (especially for many PNP this is longer). Good news is that security is running in paralel.
rejections on this stage are lower, but in some cases people do forget their original diplomas (with translation if needed).
A11.2 either it will go rather fast after R10 (within 1-2 weeks) or it will be delayed. If it is delayed, then they usually decide to contact your employer to confirm your work experience. It seems that this part is fast for most of the PNP (especially if the program already checked your relevant work experience). I would say, that here is the moment when CEC can wait long (if they try to track down your canadian employers and they have problem to do that) or have it done really fast (if work experience is easily understood). Once this part is approved (or more precisely appear to meet the requirements), whole file is forwarded to the LVO.
Rejection in this stage happens mainly from poorly written reference letters or NOC mismatch. In some cases here are the rejections for not enough CRS points. Overall, rejection rate here is not very high
LVO transfer - it can be done right after A11.2 is confirmed (and they like to do it fast in order to get rid of applications from CIO). After the transfer LVO is either just waiting for securities to be finished, or if they have their concerns they do start additional investigation (employer calls or visits and such). here the applicant can get all type of ADR - additional PCC, if you just move to a new country where you did not need PCC before but now you are there over 6 months; POF confirmed again (to see if you really keep Money ready); new medicals (if it takes too long)....
Security checks - very difficult to say the timing. For fresh Security check anywhere between 2 months and 18 months. Those that got their study / work visa recently (past 1 to 3 years), this can be done within 1 months (that is why some CEC are so fast).
Rejections here are really rare (I would assume, that the vast majority of EE applicants are not in organised crime or terrorism).
R87 check (that you are able to settle down and support yourself) It is done right after Security is finished. They take more or less the comments from A11.2 check and add comments for R87. For PNP they comment, that they want to be in their province and they also take your POF into consideration.
Rejections in this phase are rare. (I could imagine a moment when they see, that PNP has no motivation to settle in their province or when they discover that you no longer have your Money ready.
Whole process can be slowed down by family composition change (baby or marriage). New members trigger Medical, Criminal, Security (for spouse), R10 (for marriage certificate, birth certificate, passports...), causing the delay of app. 1 to several months
As you can see, as your application follows, the rejection probability will decrease.
Also R10, A11.2, LVO transfer or R87 can be only identified from GCMS notes. It seems that different officers have different habits when it comes to updating BG check status.
In my case at the date of R10 BG went to NS (checking is in progress) and when A11.2 was finished and my file was transfered to LVO it went back to NN (Not applicable). It only went to IP (processing) after I got PPR request (here different LVO have different approach).
