Cpanel created 404 page problem

[Dirty Butter]

I use cpanel on our Linux server to create custom 404 type files with an sthml extension. I'm having issues with Google "finding" pages that are incorrect, but instead of going to the error page, the wrong url resolves to /index.php and Google indexes it.

http://dirtybutter.com/plushcatalog/ = http://dirtybutter.com/plushcatalog/ CORRECTLY

http://dirtybutter.com/plush = 404

dirtybutter.com/plushcatlog/index.php = 404

dirtybutter.com/plushcatalog/goop = 404

dirtybutter.com/plushcatalog/goop.html = dirtybutter.com/plushcatalog/index.php WRONG!!

This behavior occurs on both the 5.1.5 kurouto and the 5.1.4 blueprint skin.

Can someone suggest a way to get the error pages to work correctly?