I have two tracks I wish to have panned to the center. I have separated the stereo pair and for each track selected in turn and used Modify->Audio->Pan Center. In the viewer when I double click on each track it shows a pan value of 0 but the left track comes out of the left speaker and right one out of the right.
I'm guessing you may have inadvertently mapped the odd channel to the left and the even channel to the right in the Sequence Settings by changing the default settings in the audio tab. It should look like the image below, don't change the drop-down to Stereo Monitoring: L&R.