I'm running v3.4.6 of your plugin on a v3.5 multisite install.
This morning I found I could access the home page for each of my sites, but none of the other pages from the front end. The admin pages were fine.
I was getting a generic (not WP) 404 error, so I immediately suspected my .htaccess file.
Overnight, it appears that the Better WP Security plugin added quite a few rules to my .htaccess file, but in the process completely overwrote the required multisite edits, including the '#BEGIN WordPress` comment (but leaving the '#END WordPress' comment intact.) Other rules I had added at the end of the file were not touched.
You might want to look at this.