For the past few updates of Guitarix, I have been having issues where changing the JACK server latency causes the audio output to go crazy. This seems to stem from changes that the developer has been making to the config files, because the following commands usually get things working again:

mv ~/.config/guitarix ~/.config/guitarix.backup
mkdir ~/.config/guitarix
cp -r ~/.config/guitarix.backup/banks ~/.config/guitarix/banks

These commands backup your amp/effects presets from ~/.config/guitarix/banks (which are the hard part to restore manually), and let the default settings take over the next time the application is launched.