I've exactly the very same problem with the batteries on two different iphones with two different iFixit batteries.. The battery seems to behave correctly and coconutbattery shows everything as correct. I'll contact with iFixit to check what is happening.
I'm having exactly the same problem after changing the battery on an iPhone 6. Everything seems fine with duration but not battery usage information is displayed. I also tried to check with the Xcode logs to check that but nothing meaningful. I thought it was the battery but since you replace it by an original one, I think is software related someway. Maybe corrupted database...
I fix two iPhone 6 following instructions and was easy. One of them had replaced the battery many times and the first connector of the screen (the top one, the one that you disassemble the last) was curved. The result is that the screen was full of lines and unusable. I pressed slightly with the pry bar till I straighten it and everything was OK again.
Only one question: I have iOS 11.3 b5 and the battery health tell me about the need to repair and the detailed screen tells me “—” in maximum capacity. Both iphone with iFixit batteries.