This is a topic that I’ve been asked probably a hundred times since the SharePoint 2010 bits were released. Before I get into how I solve it, I’ll provide a little back story. To quote from my upcoming book, Professional SharePoint 2010 Branding & UI Design:
There are three site templates to choose from when creating search sites in SharePoint 2010: Enterprise Search Center, Basic Search Center, and FAST Search Center. Unlike most other sites in SharePoint 2010, these sites do not have v4.master or even nightandday.master applied to them; instead, they have minimal.master applied to them.
If you have a custom master page that is based on v4.master, nightandday.master, or even one of the typical starter master pages and apply it to one of these search center sites, you notice that the search center doesn’t work properly. This is because the page layouts and pages that are created by default for these search center sites are hard coded specifically to work best with the way minimal.master is coded.
In fact, if you apply v4.master to one of the Search Centers, the search box seems to be removed from the page… when actually it is still on the page, just hiding up in the pop-out breadcrumb menu: 
As you can tell, this is less than ideal. Also problematic is the fact that the default minimal.master that is applied to the search centers doesn’t really contain traditional navigation or ways of navigating back to the parent site. So how do you get custom branding to work with the search center in SharePoint 2010? You have some options:
- Create a new custom master page based on minimal.master
- Adjust the page layouts or pages in the search center, to use the standard content placeholders
- Nick Hadlee created a nice sandbox solution to fix this problem for you. In many cases this might be the best course of action if you are comfortable using 3rd party solutions: http://sp2010searchadapters.codeplex.com/ )
I used to recommend a different solution instead of option #3 there, but now I only use the sandbox solution to solve this problem for all my client work because it just works and customers typically are ok with installing sandbox solutions.