distortion when reducing sampling rate

Dear Forum
I have been having a tussle with a project to digitize my vinyls. I have only just begun so I am very new at this. I have a Terratec USB26 Producer which does the digization on a Windows box. If I digitize at 9600 hz, 24 bit and import into Audacity I can clean, (de-click, de-noise etc). I am less clear as to the setting for the sliders for RIAA equalization. However my main problem at the moment is that when I change the sample rate from 96 kHz to 44100 Hz I get a large amount of distortion.
I use Fedora 7 on a 32 bit AMD Athalon chip. The Audacity version is 1.3.2.

ths Peter