You're talking about sample rates, not bitrates, just FYI. It's 44100 Hz, not 44100 kb/s.
The best way to do it would probably be to use an encoder that doesn't force you to use 44100 Hz wav files as input. Try foobar2k or the BlueRazorLame frontend, as I know for a fact that they will take a 48000 Hz wav as input.
If you're dead set on resampling to 44100 (which really isn't necessary), what you need is a resampler that does nothing but resample. If you're losing quality, your converter is probably doing more than just resampling, or the resampler could just suck. There may be a simpler way to do this, but my personal suggestion would be using the BeSweetGUI and running it through nothing but the SSRC resampler.
Go
here for BeSweet, which includes SSRC, and
here for the BeSweetGUI, which makes using BeSweet easier.
Extract them both and run BeSweetGUI, then use the browse button beside BeSweet.exe to point the GUI at BeSweet. After that, select your input and output files the same way. Next, make sure that only SSRC is ticked on that main page. The tooltip should say SSRC - Resampling frequency : 44100. If it doesn't, click the SSRC button over on the right and change the value in the 'set sampling rate of outputfile' to 44100. After that, you're ready to go. BeSweet should do nothing but run it through SSRC and you end up with a 44100 Hz wav file that should sound exactly like the 48000 or whatever one did.
Jam it back in, in the dark.
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