I had this same problem, and while I never found a solution to it, I did find a way around it while still being able to use Nice URLs.
I installed the "include" plugin (
http://www.dokuwiki.org/plugin:include), which will insert one DokuWiki page into another.
Once installed, click on the logo that gives you the "This topic does not exist yet" error. Create the page. On the newly created page, type "{{page>:start}}" (without the quotes).
Now, when you click on the logo, you will go to this new page, but that new page will have your start page inserted into it. It will be indistinguishable from the actual start page.
You can also have the logo go to some other page, if you wish. See the "include" plugin page for the proper syntax.