I've experienced this also.
I just opened a project in X2 to do some testing.
I noticed that the Punch in/out button was lit in the control bar and the in/out selection spanned the entire project.
Note that I have never manually turned on the punch in/out function. If I disarm the punch button and try to record, the wave form will draw and when I stop the project, the wave form and audio will disappear.
If I leave the Punch in/out button lit and try to record , it works fine. The audio doesn't disappear.
This is happening on a newly created audio track with no other takes on it.