Ya, it definitely sounds like it's just a few outliers in the group of mobs that are just getting missed for what ever reason.They could just be late to the gathering so they may not feel the effects from the early flash or a missed hit while tagging the groups.
I'm going to assume that the group as a whole is getting well established on threat. I'd suggest that while your spamming flash, to cycle through the mobs and get an idea of where they all stand on the threat tables. If you can identify the ones that have DD's catching up on you, then you can easily isolate the issue and dump more threat into those specific ones. If you come across a situation where literally every mob in the pull is about to fall off of you, then those DD's are getting some serious procs early in the pull (or just flat out ignoring quelling strikes). God help you if this is the case...
If that doesn't help, that I'd say to just shield lob literally every mob along the pulling path. This will cut down on the need to flash while running and allow more flash spams while they are all grouped up. The difference is not much but I find it easier to search through targets for weak links when I can spam flash for a longer duration.