UVG still "hint" mp4 videos when Reencode Mp4 is not checked. However, "hinting" should be much much faster than a complete encoding.
You can create a textfile, Log.txt, in \DesktopModules\UltraVideoGallery folder, which will then be filled by UVG.
Maybe you should clear the encoding queue again, upload some videos, and let UVG fill log.txt. When it get stuck again, send me the log.