Are you using multiple master templates for multiple site collections in SharePoint 2007? By default all search results are sent to "/_layouts/osssearchresults.aspx" for MOSS installs and to "/_layouts/searchresults.aspx" for WSS-only. The result is a search results page using the hardcoded "~/_layouts/application.master" master page and default theme; this is not good.

Solution:

1. Go to the base of you site collection and "Modify All Site Settings". Near or at the top right you will find "Search Settings".
2. Select "Use custom scopes"
3. Enter a new path, I choose to use: /{sitecollectionbase}/SearchCenter
4. Create new folders via sharepoint designer where nessesary
5. Copy file osssearchresults.aspx from c:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\TEMPLATE\LAYOUTS to your new folder location.
6. rename osssearchresults.aspx to Results.aspx
7. Edit Results.aspx to reflect the master template and other required changes needed.