CSS file being loaded twice

From firebug I can see that in our SharePoint 2013, tokyo.css is being loaded twice. Once before my custom.css is loaded and once after. This is causing my customization to be overridden by default styles in tokyo.css

This is what I have in the master page:

<SharePoint:CssRegistration Name="<% $SPUrl:~sitecollection/Style Library/~language/Themable/Core Styles/tokyo.css %>" runat="server" EnableCssTheming="true" />
<SharePoint:CssRegistration ID="CssRegistration2" Name="/SitePages/css/custom.css" runat="server" After="<% $SPUrl:~sitecollection/Style Library/~language/Themable/Core Styles/tokyo.css %>" />

What am I doing wrong?