To answer your first question...
Browse to the page with your module on it where the video doesn't play, view the source of the web page and take a look at the HTML markup to make sure the path the file is correct and that the HTML looks correct.
To answer your second question...
do the following..
first, make sure you have a /Portals/#/RepositoryTemplates folder. If you do not, create one
then, copy the /DesktopModules/Repository/Templates/NiftyVideo folder to the /Portals/#/RepositoryTemplates folder so you end up with a folder named,
/Portals/#/RepositoryTemplates/NiftyVideo
now, edit the template.html file in that folder.
You'll see the object tag for the player, just replace the object tag with the HTML markup for whatever video player you want to. Take notice of the tokens that are used to represent the video file to be played, and just use the same token in your new HTML markup.