I just installed IWS8.1 on a new PC for our application. I copied the whole project folder over from my laptop where I did the initial project development. All of the comments are being deleted from the Screen Scripts after I edit the script and test run the project. Some of the screens still have the comments, it seems to remove them after I make an edit. The new PC is a HP Pavilion tower running Windows 10. My laptop is a Dell running Windows 10. My other scripts are not affected so far.
I notice that if you make an edit to the screen and save it. The screen script comments will disappear. If you close the screen and re-open it. The comments will re-appear. So it looks like the real problem is if you make an edit and save the screen twice. At that point, the comments will disappear permanently.
Short term solution: Every time you click 'Save' or 'Save All', close all of your screens.