In my experience, you need to keep an eye on videopad, especially to what it is doing elsewhere on the time line when working zoomed in.
Often things get misaligned when you're making small changed. Example: Items on track two are no longer where they are supposed to be.
This happens most likely because of the auto ripple feature. I find it useful to place "markers" on the time line.
I'm talking about a stack of audio and video clips that needs to stay aligned. I place them on strategic placed on the time line and check them now and again.
If they become misaligned I press ctrl-z and repeat the edit.
Most of the time I should have held the shift key before making the change.
But sometimes videopad just screws with you. So you better keep an eye on things, and save often, and to different file names so you can rollback.