I had the same problem. Jumping to next line with <enter> simply generated an extra empty line at the end of the subtitles.
Instead, simply hit <control><enter>
That will eliminate the extra lines generated by VideoPad. Each time you hit <enter> an EXTRA line is generated by VideoPad. That puts extra lines at the end of your lines. To eliminate, use <Control><Enter> to jump to the next line.
One thing though, after you skip to a new line with <control><enter> the system stops recognizing the second line as a new line so the alignment (like centering) stops working! Everything becomes left aligned.
I am using MacBook Pro
VideoPad V: 8.4