Ok So I'm running into this issue also.
The 3rd party batteries in question giving me issues are the Opteka brand which are carry overs from my 7D.
in 2013 I bought a Canon LC-E6E battery charger through Amazon UK and had this shipped to my mothers house in the UK (I live in Florida) was getting ready for a trip so decided I would get this sent ahead of time and be there waiting for me.
Battery charger that came with my 7D was the USA version (LC-E6) with the two prongs that flip out and allow it to be plugged into the receptacle in the wall.
The nice thing about the LC-E6E was that it was auto switchable between voltages and Hz depending on the countries, all that was needed to be changed out was the cable, for the respective country. Great charger why doesn't Canon ship these standard with all cameras, regardless of where in the world, would be cheaper for canon production wise to have "one global unit"
Cool, now I can now charge two batteries for my battery grip.
So move on to 2015 bought a Canon 7D MKII, low and behold it comes with the LC-E6E charger. so now I have two, excellent much better system. (or so I thought)
OK so I have two genuine canon batteries, 4 sterlingtek and 4 opteka batteries.
The canons and Sterlingtek batteries charge ok in any of the 3 canon chargers.
The opteka batteries have started giving me issues, but after trial and error have determined that it is only in the 7D MK II LC-E6E charger, but after using the business card trick on the contacts and trying in this newer LC-E6E charger numerous times, its still giving my the constant blinking LED.
So I tried these Opteka batteries in the older LC-E6E charger and the old LC-E6 charger (flip out two prong USA charger) and they are now charging fine.
So i've come to the conclusion there must be something updated in the electronics of the newer charger. So my advice is to follow the advice posted here about cleaning the contacts, if you're going to buy 3rd party batteries I would stick with the Sterlingtek's for right now.
I wish Canon would drop the price of their batteries, so that we would not have to resort to using the 3rd party batteries.