Some weird stuff is happening, I am converting an application that used to use javascript to open another web page in a tiny window for data input to use a ModalPopupExtende
For me the solution was to get the modal poup out of the main update panel. Once I did that the commas went away. If you truely need an update panel inside of the modal popup, create one of it's own inside that panel.
I did not need to roll back to previous version of the toolkit.