I was incorrect in describing my version number. It is actually 13.61 I am using, the last update I was entitled to within the 6 month window of purchasing this copy. (I do have several previously purchased versions too!) The two images in this screen show the project prior to saving with a fade in which had been created using the "start of clip to cursor point" mode. Nothing more was then done except to close the project, clear the cache files then re-open it. The fade in (and a similar end of project fade out) had disappeared. I haven't had time to download and try the latest release as I've got a lot of editing to get through right now.
http://phmusic.co.uk/misc/VideoPad-13_61-FadeSave.jpg