I've never worked with pocketsphinx, but maybe http://cmusphinx.sourceforge.net/wiki/tutorialam http://cmusphinx.sourceforge.net/wiki/tutorialam or
http://cmusphinx.sourceforge.net/wiki/tutorialam can be of help.  Are you also recording your voice in 16-bit 16kHz single channel mono as stated?

I found an example on http://people.csail.mit.edu/hubert/pyaudio/#examples which I think has the necesarry options. I guess you'd have to change the CHANNELS to 1 and the RATE to its 16kHz equivalent.
"""PyAudio example: Record a few seconds of audio and save to a WAVE file."""

import pyaudio
import wave

CHUNK = 1024
FORMAT = pyaudio.paInt16
CHANNELS = 2
RATE = 44100
RECORD_SECONDS = 5
WAVE_OUTPUT_FILENAME = "output.wav"

p = pyaudio.PyAudio()

stream = p.open(format=FORMAT,
                channels=CHANNELS,
                rate=RATE,
                input=True,
                frames_per_buffer=CHUNK)

print("* recording")

frames = []

for i in range(0, int(RATE / CHUNK * RECORD_SECONDS)):
    data = stream.read(CHUNK)
    frames.append(data)

print("* done recording")

stream.stop_stream()
stream.close()
p.terminate()

wf = wave.open(WAVE_OUTPUT_FILENAME, 'wb')
wf.setnchannels(CHANNELS)
wf.setsampwidth(p.get_sample_size(FORMAT))
wf.setframerate(RATE)
wf.writeframes(b''.join(frames))
wf.close()
[\code]
Again, I've never worked with this or audio in general so I'm making some guesses based on the documentation and interwebs.

That seems like the kHz setting to me. Have you tried setting it to 16000? That's all I can think of. What are you trying to make btw, a secure Skype clone?
j/k really though, what are you making?

That would be epic indeed. It seems to have something to do with the stream itself e.g. opening a surround stream on a stereo device won't work.
I don't know what could be wrong though. Could you maybe paste your script?