I had the same problem too but I managed to figure out what I was doing wrong. This is what I did to make it work
Extract the files from (nextgen-gallery.0.96) and create the nggallery folder in wp-content/plugins/.
Open the nextgen-gallery folder and upload all the content including the imagerotator.swf file to wp-content/plugins/nggallery/.
I’m assuming that you would have downloaded and extracted the imagerotator-3-16(imagerotator.swf) file.
Upload the imagerotator.swf file to wp-content/plugins/nggallery/ to overwrite the one thats there. After doing so the plugins should show up in my plug-in menu.
Enjoy
