In case it matters to anyone else, I got a timeout error running the IPNCheck script. The timeout occurs on the fsockopen statement. I just found that I am also getting a timeout error on an fsockopen statement in another (non-Zen) site on the same server, and that is not when trying to connect to Paypal. I think it that case it may be trying to hit the USPS site for postage information. So I am opening a ticket with the hosting company to see why the outgoing communications are not working.
I think they recently upgraded the server software (Apache), so maybe some default settings were changed.