A question about the MMC5 & NES original PCM.

So, I've made a couple of demo PCM programs, like 7-bit 44KHz ones and MMC5 8-bit 22KHz ones. But one guy, after recording the sound from FCEUX and comparing it with a regular wav file using some software, says there seems to be some distinguishable differences.
Is that the emulator/recording problem, or it is my problem, or the limitation of the NES?
Sorry to say I know few about the software he uses, and I can only report what I know.

(In the making of the programs, I simply converted those sound files to wav files, removed the headers, and then in the case with 7-bit PCM, right shifted every byte by one bit.)

FCEUX is running a bandlimited sound synthesizer, with things like filters and DC cancellation, so its output isn't going to match the input identically.