Ok, figured it out I think. We use a js functions in the Javascript/KartrisInterface.js to close modal popups. The names of the elements that these operate on have changed slightly:
For example:
cntMain_UC_ProductView_tbcProduct_tabMain_fvwProduct_UC_PopUpLargeView_popMessage
Basically, the ct100_ part at the start of all the elements is now gone.