I have a similar problem. Here, it is the tabrow background colour that is different in both web and server view.
In the server, I have set the tabrow background colour to white (RGB 255,255,255) and it is shown a white tabrow background. However, in the webview the tabrow background appears in a kind of blue/gray - clearly different from the specified white.
We are using QlikView Server 11 on a Windows Server 2008 R2 server and we use the nobar file extension to hide the AJAX toolbar.
Have you got any ideia on what can be causing this mismatch?
Thanks in advance.