The Web Access module uses a different location to store what weekdays are and which aren't. You cannot remove weekends from the graph, this is a much requested feature and according to the admin comment it is coming soon.
UNDER REVIEW · Visual Studio team
Visual Studio team (Product Team, Microsoft) responded · Aug 22, 2013:
We’re starting work on this and should be able to close it down soon. Stay tuned.
It might ship with TFS 2013 update 2 if they managed to fix this.
Update
TFS 2013 update 2 RC now has the features to set Team Days off, which will effectively hide the weekends and these team days off from the burndown chart.
Non-working days – Starting with Update 2, you can define you’re non-working days (weekends, for most of us) and we’ll exclude them from the burn down calculation so it no longer looks like you are on track when you really aren’t (because you don’t plan to work the weekend :)).
http://blogs.msdn.com/b/bharry/archive/2014/02/05/vs-tfs-2013-2-update-2-ctp-released.aspx