Taking the FFT of a sinusoidal signal and going back
Part of the problem is that you are using sine waves.  The imaginary components of an FFT result contains all the information about pure sine waves (e.g. that are equivalent to a sin() function that starts with phase of zero at the start of the FFT aperture, and that are exactly integer periodic in aperture).  If you use only the real part of an FFT result, you can only see cosine waves (not sine waves, periodic in aperture), thus your silent result.  

For shorter FFTs, the real component of the result might contain windowing artifacts if the frequency of your sine wave is between FFT result bins for the given FFT length (e.g. not integer periodic in aperture).  So, in synthesis, you are hearing an artifact, quantized in frequency.