Hello,
Usually we see this with Group policy updates. More information on them can be found here:
docs.microsoft.com/.../cc940895(v=technet.10)
Specifically, I would like to point to the tip at the bottom:
Consider notifying users that their policy is updated periodically so that they recognize the signs of a policy update. When Group Policy is updated, the Windows desktop is refreshed; it flickers briefly and closes open menus.
Dynamics GP will run into this same issue, although usually it is simply window flickers, and nothing closes. I would check Group Policy and make sure that it is not updating too often. If it is updating every minute or more often, then it may interfere with users.
There are some other possible causes (antivirus scans, third party oddities, other random environmental effects), but I recommend checking this first, as it is the easiest to review.
