I'm having the same problem. No matter where I set the noise floor - using the calibration method or manual - Golden Records just does not pick up certain parts of certain records, even though the playback sound (I've tried playback sound ON and OFF) is consistent from the vinyl source device.
I use NCH's Wavepad and Soundtap and they are fine. But I'm finding Golden Records more hassle than it's worth. I'm thinking of going back to EZ Vinyl Converter, even if you have to use iTunes (my old EZ converter eventually died after many years' solid use).
If I can solve this problem, grea