Adding the same control to more than one page(though Footer.ascx is a user control) must not be an issue.
Anyway i dont think the way you have added the control to the master page is correct. You have placed the 'nopCommerce:signup' control inside a contentplaceholder in the master page. Content placeholders are added to master pages so that Webcontent Forms can use content controls (eg:
<asp:content contentplaceholderid="cph3" />
) to place its own html.
You must add a web content form to your project, specify the master page and then add your control into the added web content form.
If something else is the issue please provide more details regarding how you are using Footer.ascx and Three.master to display
<nopcommerce:signup id="signup" runat="server" />