I set up Pulse resampler. But, if you output directly to alsa (bypassing Pulse), you need to configure resampler in alsa too. I believe in alsa default 44100. Therefore input 44100 and 48000 will be resampled to 44100, and afterwards hardware resampled to 48000 again = distortion every time.
Maybe Audacity at boot disables Pulse or change it into a strange mode and only work alsa before rebooting?
Audacity changes the sound settings at startup, it’s not normal. If your sound card has a high quality resampler - you will not notice a problem. But Audigy 2 ZS is a litmus test. You can configure alsa to 48 kHz I suppose. But this does not change the strange behavior of Audacity.
I suggest test: Set up Pulse resampler to 48 kHz. Run Audacity and close. Open audio file RMAA tones 48 kHz in audio player like Audacious. Connect the line output - to the line input of another sound card of another computer, record and check the spectrum. 22 kHz (44.1 kHz) or 24 kHz (48 kHz) actually plays the computer with Audacity.