Thread:Project:Support desk/Short URLs: some links to Special pages don't work/reply

Logout link is: /index.php?title=Special:UserLogout&returnto=currentpagename

This URL scheme should work for you, since it's the same as when you edit a page:

/index.php?title=currentpagename&action=edit

Those URL that point to index.php shouldn't be affected by rewrite rules.