domain mapping stops shopping cart from working

I have Marketpress set up on a multisite website enabled using a global cart, and now I have set up Domain Mapping for one of the subsites. Since setting it up my global cart has stopped working. I can put items into my cart, but they disappear when I go to checkout through my root site.

I've read a lot of other people have this same issue but I they all seem to stop responding and I don't see a way to solve this.

I believe it to be either an ajax or a cookies issue, either way how do I resolve it?