Weak pull-up resistors

You have conflicting statements;

--- Quote Start ---

I haven't connected these pins to anything yet.

--- Quote End ---

vs

--- Quote Start ---

I enabled weak pull-ups for the input and output pin (cyclone II device).

--- Quote End ---

If you haven't connected anything yet, then neither pin can be an output. If you have defined a top-level entity with your inputs and outputs listed, then the outputs will need to be driven. The low you see on the output can be due to you driving it, or, it can be due to a synthesis setting.

Older generation devices had a default unused pin setting that would drive the unused signals as output to ground. Newer devices default to as inputs tri-state. To see what mode you are using, in Quartus, select Assignments->Device, Device and Pin Options, Unused Pins tab. Select as input tri-stated, and then place-and-route your design, and then re-measure your pins.

Cheers,

Dave