When you create a new tool and give it a page of its own (http://127.0.0.1/5335/myNewToolName), the template you get is really plain - just enough HTML to get your page to validate (maybe ;).
#template node in the
myNewToolNameWebsite table in your database and refreshing the page in a browser, the template changes to a very very old template (like the one on this page).
Just found the solution (in this message from 2002): you need to reinstall the tool to get it to pick up the changes. Selecting the
.root window for the new tool, then Tools | Developers | Re-install Front Tool... will do this. And now you have a tool that fits in nicely with the rest of the desktop website!