Windchill is a great program we have been using it for years now. One time we had the same problem as you guys. We found out that for some reason PTC was only working with "gmail" accounts. So we had a few of our members just make new emails (which worked out okay because now they have a team specific email account.) This even happened when we tried to add them manually as well (The non-gmail accounts never got the message invite in their email). So I would look and see if that is the problem, and see if changing the email account helps.
If it is still not working, we can help you guys figure out whats going on.
