RewriteBase is in comment.
Perhaps you have to activate the line.

I suggest that you have a look in the SH404SEF document that should explain how to setup the htaccess.

Sometime it is required to enable the line and sometime it is also required to provide another directory than the /
All depends your URL

You can also verify that SH404SEF give a correct translation between the "alias" or SEF name and the original URL. Sometime, you have to verify that when you access a menu entry you reach the correct entry in the SH404SEF URL convertion.