Hi J@r0d,
this sounds that there are issues with the samplerate.
The default alsa sample rate is normally 48kHz. Since shairport outputs 44.1 kHz alsa resamples the shairport output to 48kHz which may have a negative effect with some sound cards.
Try to edit /usr/share/alsa/alsa.conf
defaults.pcm.dmix.rate 44100
(default is 48000)
An other thing you can try is to play with shairport buffer sizes (-b option).
Try to edit /usr/lib/systemd/system/shairport.service
ExecStart=/usr/bin/shairport -w --name=RuneAudio --on-start=$ON --on-stop=$OFF --meta-dir=/var/run/shairport -b 95 -o alsa -- -d hw:1,0
Something like 95 should be a good starting point.
Do not forget to reboot your system after changing the settings.
Frank