what are you selecting rebuild missing or rebuild all? try rebuild all. I am not seeing anything in the code that prevents a multimedia file from having the thumbnail rebuilt. the same code that is in image-inc.php is in adm-misc.php
I can not say without knowing what your old broken ffmpeg was doing. The extraction of thumbnails from video is handled by ffmpeg and as long as it is in full working order it does work for the formats that it supports. As noted that varies from install to install.
There are alot of options in the software but the program is limited by your server. For instance flash upload if mod security is set on the server the flash upload will never work. Same goes for FFMPEG if its not working properly your not going to get a thumbnail. It may work for some formats and not for others.