When you create and invite in iCal, it will get mailed as a VCALENDAR attachment. iCal seems to be scripting Mail to send the invite. By default, it seem to use the first email account in mail. Ok, so far so good. Unfortunately, in the VCALENDAR invite itself, there is a meeting organizer field (ORGANIZER;CN=). That field is getting to a value determined by iCal. Unfortunately, when you have multiple mail account on your system, iCal picks whichever one it feels like. As a results, replies to your meeting invite will get sent back to this email address, which may not be the one you want (work vs personal for instance). You can end up with a mismatch where the invite attachment is sent from one account, but the email address in the vcal attachment is for another and thus the invite attendance response will get sent there.
The question is where does iCal get this information from? Is there a way to force iCal to use a particular address as the meeting organizer?