At various points of the day my WP permalinks keep breaking. When I'm using custom perms it works but then a few times during the day it just throws a Page Not Found. I fix it by setting perms to default, then back to custom and it works fine.
My Sys Admin can't figure it out. Hopefully a guru can lend some help?
The problem is indeed most-likely the sCategory Permalink plug-in (the one that gives you /%scategory%/. 404s are somewhat common. Go to Options | Permalinks page in Site Admin and click Save Changes to regenerate permalinks. They way to confirm this is to use WP-default permalinks to test behavior. If all is working well, it is the sCategory Permalink.
If this isn't working, publish your .htaccess and that will help us troubleshoot better.