Sounds probably like it might be to do with whats running, and possibly some settings in the Line 6 Audio-Midi devices box.
You may have already tried these things before so please forgive me in advance.
If you haven't tried these things, have a look at the vids and pdf on this page:
This might help your audio.
You could also adjust the buffer amount by going to the Line 6 folder and in the tools folder open Line 6 Audio-Midi devices. If you move the lever to the right one spot you will get slightly more delay between hitting the string and hearing the tone, but this can help with issues where audio is cutting out. If it still doesn't help, move it again etc.
Here is a page which looks at some other things to try and the buffer things too:
I hope something will help with your audio. Let us know how you go.