I have a traffic manager instance on my account. I can see it in https://manage.windowsazure.com but not in https://ms.portal.azure.com. Wh

Because the new azure portal YET do not have support for Traffic Manager. If you click on Traffic Manager in ms.portal.azure.com you will see a message clearly stating as below -

So this means you will have to use manage.windowsazure.com only to manage Traffic Manager stuff as of today.