I'm not sure if this is a beta specific thing, but since I'm using a beta I'll report it in this forum.
If I edit a waypoint in 1.65, the waypoint's timestamp is lost. To see this in action, open the Edit Waypoint dialog from the WayPoints tab of a file properties dialog. Press OK (with or without changing anything) and then press Refresh in the Properties dialog. The timestamp is gone.
As an aside, I notice that if I change nothing in an Edit Waypoint dialog and press OK, the file is marked as changed. This is true even after the timestamp is already gone.