Yes - hundreds of lines of code all included within comment tags. My guess is that someone added the commented code with the intention of removing the comment tags at some point and thereby subverting the site.
The problem seems to have been nipped in the bud. No further evidence of tampering since the initial incident. I attribute the security hole as having something to do with the way I was accessing the site while I was in Toronto; password changes seem to have done the trick.