How to switch on "weak pullups" for Cyclone in Quartus 10SP1

I didn't clearly understand from your post, if the reported problems have been with other pins than CLK0 (pin 10). With other pins, weak pull-up should work of course. But the resource property editor isn't the right way to do it, it's only intended for changes to a compiled design. You have to use either the assignment editor or the convenient pin planner. Columns showing the respective properties can be enabled in the pin planner.