I had the same issue under Sense 5 roms.
With the phone on and charging I never reached more than 60% of battery even using battery optimizer.
The solution for me has been back to a 4.2 AOSP Rom (ICJ in my case) and a couple of cycles again my battery works as usual.
I tried again with a S5 rom and the issues are back, so I have to use no Sense 5 roms if I want my battery right.
You can also try to charge in Recovery, that worked for me, to wake the bootloader.
Hope this would be useful for you.
PD. Sorry for my english :P