My N5 with the stock 4.4KK works fine with wireless charging.
I wanted a bit more out of my device so I installed a few different roms over the course of a couple weeks and decided to stick with CM11.
I haven't tried any rom with a stock kernel, so I'm going to try that next. What I've noticed is that with any ROM installed that is not stock, and with ElementalX Kernel, wireless charging no longer functions.
Is there something I'm missing somewhere? If you have a link to a discussion pertaining to this issue, please post it up so I can do some reading.