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Search Box in the chrome works differently then any other place in the product. If you look at default.master(%Program Files%\Common Files\Microsoft Shared\Web Server Extensions\12\TEMPLATE\GLOBAL) file you can find the following

So basically the search box is hosted by delegate control. Essentially the idea here is that WSS comes with a search box which supports certain features. When you install MSS or MOSS a newer Search box feature is installed with higher priority) and the delegate control know to pick this up. You can read more about the delegate controls here:

http://msdn2.microsoft.com/en-us/library/ms463169.aspx

Create a new feature that will put the search box with correct properties that you want: Follow the steps in

http://msdn2.microsoft.com/en-us/library/ms470880.aspx

In step 3 in the linked article instead of using what is specified in the article use this

<?xml version="1.0" encoding="utf-8" ?>
<Elements xmlns="http://schemas.microsoft.com/sharepoint/">
    <Control
        Id="SmallSearchInputBox"
        Sequence="21"
       
ControlClass="Microsoft.SharePoint.Portal.WebControls.SearchBoxEx" ControlAssembly="Microsoft.SharePoint.Portal, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c">

      <Property Name="GoImageUrl">/_layouts/images/gosearch.gif</Property>

      <Property Name="GoImageUrlRTL">/_layouts/images/twg/goRTL.gif</Property>

      <Property Name="GoImageActiveUrl">/_layouts/images/gosearch.gif</Property>

      <Property Name="GoImageActiveUrlRTL">/_layouts/images/goRTL.gif</Property>

      <Property Name="SearchResultPageURL">/_layouts/osssearchresults.aspx</Property>

      <Property Name="UseSiteDefaults">true</Property>

      <Property Name="FrameType">None</Property>

      <Property Name="DropDownModeEX">ShowDD</Property>

      <Property Name="ShowAdvancedSearch">false</Property>

    </Control>  
</Elements>

You do not need to do step 4 and 5 in the linked article. Note that I have changed the sequence number to 24 which will ensure that your control is what the delegate control render. It should be between 0-25 as the OOB search box has a sequence 25.

The property that I added is highlighted in green.

The value is ShowDD by default if nothing is set.