I think that you dont have the pathing set up correctly. I had some issues w/ the whole style sheet thing. Instead i found out about themes and they are worth looking into.
Here is how i have mine set up.
The mast page is at the root of the web. You could really have this anywhere you want it. Then i created the folder
App_Themes (This is a special .net folder such as App_Code, App_Data)
In the App_Themes Folder you add a new .net folder ( a theme folder is the only folder you can add at this level). I have two themes (Black, White).
In each Folder i have my .css file for the whole site plus an Images folder ( in this level you can actually add a folder).
Now in my web.config page i have this code
This tells the site to use the .css sheet associated with the Black theme.
So in the end i have to themes set up which means i have 2 different css files for the site. Depending on which 1 i choose it will completly change the way the site looks and feels. THis is the great thing about Themes.
You can also change themes in code. So you can have like a user settings and allow the user to select which look they want.
You have to set this in the Page_PreInt sub. ..
Protected Sub Page_PreInit(ByVal sender As Object, ByVal e As System.EventArgs) Handles Me.PreInit
Page.Theme = "White"
Hope that helps