Has it ever happened to you that you've enabled all the steps of URL rewriting, and it's working properly for some pages but not for others?
In my case, i've gone through all the usuals: (enable URL re-writing in joomla, renaming .txt, to .htaccess) it works as expected for pages that are opening from simple menu navigation, but not from pages opening from a rocksproket mosaic.
On total brain fart mode, but here's what it was happening.
The rocksprocket had custom URLs set for these menu items so it was still pulling the index bit. It worked as expected after I fixed the entries in the fields.
I don't know if this is of any use to anyone, so up to you if you want to delete!