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Header Missing in Email Template sent using an Assignment Rule

I'm facing a strange issue. I have a Lead Assignment Email Template which has both Header(with a logo) and Footer.
Im using this in some workflows and in Assignment Rules. Whenever workflow is triggered an Email is sent. The Email which I get is proper with the header and Footer(i.e in HTML Format). But the problem is with the Email sent automatically using an Assignment Rule.Both header and Footer are missing and the template doesn't seems to be like HTML.
Im testing this in the Sandbox.
Can any one help me to resolve this issue?
Any pointers will be of great help.
Thanks in Advance.