I had the exact same problem and managed to reproduce it in the ChatterBox sample app if I set Visual Studio to native debugging and at any point stepped through the code.
Also, closing the App without going through the "Stop" procedure and stopping the AudioClient will require you to restart the emulator/device before being able to capture audio data again.
It nearly drove me nuts before I figured out the before mentioned problems but I finally got it working.
So..
1. Be sure to NOT do native debugging
2. Always call IAudioClient->Stop(); before terminating the App.
3. Make sure you pass the correct parameters to IAudioClient->Initialize();
I've included a piece of code that works 100% of the time for me. I've left out error checking for clarity..
LPCWSTR pwstrDefaultCaptureDeviceId =
GetDefaultAudioCaptureId(AudioDeviceRole::Communications);
HRESULT hr = ActivateAudioInterface(pwstrDefaultCaptureDeviceId,
__uuidof(IAudioClient2), (void**)&m_pAudioClient);
hr = m_pAudioClient->GetMixFormat(&m_pwfx);
m_frameSizeInBytes = (m_pwfx->wBitsPerSample / 8) * m_pwfx->nChannels;
hr = m_pAudioClient->Initialize(AUDCLNT_SHAREMODE_SHARED,
AUDCLNT_STREAMFLAGS_NOPERSIST | AUDCLNT_STREAMFLAGS_EVENTCALLBACK,
latency * 10000, 0, m_pwfx, NULL);
hr = m_pAudioClient->SetEventHandle(m_hCaptureEvent);
hr = m_pAudioClient->GetService(__uuidof(IAudioCaptureClient),
(void**)&m_pCaptureClient);
And that's it.. Before calling this code I've started a worker thread that will listen to m_hCaptureEvent and call IAudioCaptureClient->GetBuffer(); whenever the capture event is triggered.
Of course using Microsoft.XNA.Audio.Microphone works fine to, but it's not always an option to reference the XNA framework.. :)