[eluser]WanWizard[/eluser]
You first have to understand the problem before you can have a solution. And I think I described the problem.
So, do these two sites share the same session? If so, then fix it by making sure both sites have their own session, or or fix the cart library as I described if you require the session to be shared.
If you want me to fix it, fine, send me a PM and we'll discuss my hourly rate...