Okay so fixed it!

I coded a control adapter to set the href correctly.

using System;
using System.Collections.Generic;
using System.Linq;
using System.Web;

namespace JR.EPI.OAPMain.WebForms.ControlAdapters
{
    public class LinkControlAdapter: System.Web.UI.Adapters.ControlAdapter 
    {
        protected override void Render(System.Web.UI.HtmlTextWriter writer)
        {
            System.Web.UI.HtmlControls.HtmlLink HL = this.Control as System.Web.UI.HtmlControls.HtmlLink;
            if (HL != null)
            {
                HL.Href = VirtualPathUtility.ToAbsolute(HL.Href);
            }
            base.Render(writer);
        }
    }
}

and added a browser file in App_Browser folder.

<browsers>
    <browser refID="Default">
      <controlAdapters>
        <adapter controlType="System.Web.UI.HtmlControls.HtmlLink"
                 adapterType="JR.EPI.OAPMain.WebForms.ControlAdapters.LinkControlAdapter, JR.EPI.OAPMain.WebForms, Culture=neutral, PublicKeyToken=null" />
      </controlAdapters>
    </browser>
</browsers>

Not sure why VirtualPathUtility.ToAbsolute(HL.Href) works where the HtmlLink's RenderAttributes call to REsolveClientUrl does not but hey as long as it works right!

Michael.