Sounds like you need to setup your virtualhost with ServerAlias(es) in apache.
where you setup your dekiwiki apache config, probably in /etc/apache2/sites-available/dekiwiki
add ServerAlias line for each wiki you want to run. Like this...
<VirtualHost *>
ServerName server1
ServerAlias wikiapples
ServerAlias wikipears
ServerAlias wikibananas
(rest of config.....)
Additionally, you need to setup DNS so that your aliases resolve. For testing purposes, you can cram the names to resolve to the same IP in your static hosts file in your client OS.
(I'm saying the names server1, wikiapples, wikipears, etc, all need to resolve to the same IP somehow.)
Once you've got this stuff setup, then apache will be able to pass the alias being addressed to the API, which then will know which is the appropriate database to access. If you don't do these steps, obviously the whole setup can only ever know about the instance tied to the "default" header.
Here are PeteE's notes on this subject.
http://wiki.developer.mindtouch.com/...i-Tenant_Setup