The Devel module query log appears correctly (at the bottom of the page) when I use one of the default themes, but not when I switch to my custom theme. The query log seems to appear within the inner pages in the custom theme, though not the front page or administrator pages (if those are set to use the custom theme).
I have been through page.tpl.php and html.tpl.php and I can't see any missing variables.
How does the query log get printed on the page?
admin/config/development/devel
Also go through the permissions of the user that you are checking. Make sure you are checking with admin – Swinneydpm($variable)
? Did you ensure to print$messages
in your custom theme? – Tyranny