I'm using this htaccess for removing index.php on an ExpressionEngine MSM site http://d.pr/n/RZTo
It does what it needs but won't allow me to access the site via a masked CP (which I need for using the Mountee app.
Any ideas why I'd get a 404 when I try to hit the /admin.php for the site?
The secondary MSM site is under a sub-folder of the primary domain.
I've got a similar set up to you but in the htaccess for the second site, I don't have a rewritebase rule and have RewriteRule ^(.*)$ /index.php?$1 [L]
(i.e. no reference to the folder name).