I started looking at the system variables for AutCAD P&ID 2013 for publishing. I tried setting PUBLISHCOLLATE to 0 instead of the initial value of 1. That seems to have done the trick. I've been able to publish using the same old page setups that I've been trying since AutoCAD P&ID 2013 was installed. All sheets publish without errors. Publish seems to fail after the first drawing when PUBLISHCOLLATE is set to 1.
I can't get the publish command to fail on my machine here.
I tested with PUBLISHCOLLATE and BACKGROUNDPLOT set to various configurations and I always get all drawings published.
Anyway, I am glad your issue with plotting was fixed with the PUBLISHCOLLATE variable.