I solved my problem..
The problem was caused by the application i used to record the data, and the method i used.. I used Audacity, which supports the old windows MME audio API, and the DirectSound API. These are relatively high-level API's apparently, and are the cause of the distortion. About the Windows Core Audio APIs
Instead i used another program, called Reaper, it has an option to record using ASIO og WASAPI. This solves my problem. I've checked every sample in an 2 hour .wav file, using MATLAB, and it is completely bit-perfect.
I was probably some quantization error, but it was caused by the API. ASIO and WASAPI gave me bit-perfect sound, MME and DirectSound gave me a distorted signal.