Low Pass IIR filter attenuating all frequencies
You say that sampling frequency is "about 20kHz" (perhaps exactly 22.1kHz, typicaly for audio?).  So the period of a 1kHz sine wave should be about 20 samples.

But your data has a period of 6 samples.  It isn't 1kHz, but more like 3.5kHz.  Getting somewhat close to the corner frequency, although not close enough to explain attenuation by a factor of 5.

Looking at the screenshot, though, every second value is zero.  So your frequency is just under fs/2.  And that is solidly in the stopband.