Well….regardless of the source, you should just never have anything before the doctype, or else your site will be screwed up in IE (not to mention your code is just not valid). It’s great that you never had issues with the template before, but this time you do, so if you want to keep using the same template, then you’ll experience problems.
I mean, it’s up to you. Generally, if you feed IE valid code, things will be fine. But once you feed IE some invalid code (such as having something/anything before the Doctype), then you’ll have to accept likely funkiness.