Some 'auto cleaners' seem to degrade the final recording. They have an algorithm which searches for what it thinks are pops & scratches but quite often gets it wrong and removes a correct high spot, it also removes what it thinks is rumble or hiss and the final result is very flat.

The only way to achieve best results is to use an audio editor that will allow you to display the whole track as a waveform. You can then cut this down to display about three seconds of track and play this three seconds whilst the timeline is showing where you are.

When a scratch or pop is detected you can zoom in even further and remove it easily with a drag and cut ( after a while you get to recognize bad waveform and can remove it without further zooming ).

It's a very long and time consuming process but at the end you have as near a perfect recording as you can get.