Tyler Holmes has an old post on his blog that I felt is with worth mentioning as I faced this problem on a recent project and it is not the most intuitive behavior (but with SharePoint, what is?).
SPWeb.Groups vs. SPWeb.SiteGroups [Tyler Holmes]
SPWeb.SiteGroups Versus SPWeb.Groups
.NET, Microsoft, Office, Sharepoint Server, Visual Studio 2005, Visual Studio 2008, Windows SharePoint Services
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