Admin panel busted 4 network & main blog only

I have s2member set up on a multisite configuration. Got things set up entered paypal info for sandboxing and noticed the payment button generators weren’t working. We’re using multisite as we have an online magazine and social community and due to a couple conflicting plugins it made sense to use multisite to separate them so that everything plays nicely together.

Well went I created the new sub-blog for the magazine and went to s2member I noticed that it looked as it should unlike on the primary domain (the / account) where s2member lacked the prettiness and had broken functionality. I also noticed on the sub-blog that the paypal button generator worked.

So I took another look and noticed that in the network admin dashboard and the dashboard of the primary site (/ directory) where things are broken I opened under web inspector I get this in both the network admin and the admin area of site 1:

SyntaxError: Unexpected token ‘<'
mywebsite.com line:1

The other sub blogs I set up to test seem to work fine. s2member works as it should, no problems in the dashboard. It's kind of left me puzzled…

I've disabled all the plug ins and went to the twenty twelve theme, uninstalled and reinstalled s2member, and frankly sort of perplexed about this one. Has anyone else ever seen this?