What code did you use for create the control?, did you make the includes of the mojo portal namespaces?.

include this in your control

<%@ Import Namespace="mojoPortal.Business" %>
<%@ Import Namespace="mojoPortal.Business.WebHelpers" %>
<%@ Import Namespace="mojoPortal.Web.Framework" %>
<%@ Import Namespace="mojoPortal.Web.Controls" %>
<%@ Import Namespace="mojoPortal.Web.Editor" %>
<%@ Import Namespace="mojoPortal.Net" %>

and then include the control in the portal using the admin features

master page is not affected by CSS cache, most likely the change you are making to the layout.master file is causing an error so it loads a failsafe master page to prevent crashing the page. You should look in the mojoportal error log for the error

Administration > System Log

most likely it is because you are not registering your control correctly.

you should not be using <portal: as a prefix for your custom controls

this page has information at the bottom about how to register a custom usercontrol inside layout.master

http://www.mojoportal.com/usercontrols-as-include-files.aspx

Hope it helps,

Joe