I am having the same issue (I cannot save an edited video in any other format but .vpj). I did see the post above from Borate. I uninstalled the version I had, removed the videopad folder from %appdata%\roaming\NCH Software folder, deleted %appdate\local\temp files, Made sure there was no videopad folder in c:\program files (x86) folder, and restarted my machine before installing the version from the link above. I then successfully registered it. (Margin does state 'VideoPad Professional v 17.07") I did run the 'check for updates' command (there were no updates), I then started my edit from scratch.
The failure appears pretty much immediately after clicking 'create' on the options page. I noticed there was a log folder in %appdata\\roaming\NCH Software\Videopad...however there are no entries in the log folder. The video file I'm attempting to save is 6 min 8 sec long. It was originally an mp4 file saved from youtube. The edited file is on one track, beginning and ending set, no other video or audio snippets in the edited video track (track1) and nothing in any of the other tracks. All gaps are closed on the track. I did lock the track. I've tried saving both uncollapsed and collapsing the track. It was originally an mp4 file saved from youtube,
I have worked on other mp4 files downloaded from youtube and, as long as I do not use the split tool (only just cropping and/or selecting the beginning and ending for the file), I am able to save as .mp4 (and other formats).
It seems like there is an issue with the encoding applet that videopad is using.
Tal