WaveIn with Kiss FFT output has periodic errors

I'm working on a project that involves receiving audio data on Windows through the Wave In API and producing a frequency spectrum with kiss fft. The input device is the stereo mix on a Windows 8 laptop. When nothing is playing, the Wave In API outputs numbers in a range of about -5 to 5 (in a signed short variable) which is seemingly negligible noise. When music is playing, the output seems to be correct. However, when I run the output through kiss fft, the lowest frequencies have large offsets. This occurs whether or not anything is playing.

Here is the kiss fft output when nothing is playing: https://drive.google.com/file/d/0B33_0mkAWVhcTlllVEo5MzNRSFE/view?usp=sharing

I tried running the data through a hanning window and no window, and the issue is there regardless, but it is more spread out when the hanning window is applied.

When I send kiss fft an array of 0s, it outputs 0s as expected.

The code for this project is very long, but I can provide specific snippets if there are any questions.

Thanks in advance for any help.

-Eric