Not sure if this is a bug or not - when I click "calculate optimal size" under Panorama Properties, a partial width, cutting size, etc. are populated. I save and exit. Next time I go to that area, the original settings are there, not the new calculated sizes.
This is not the normal behavior. Clicking on "Compute optimal size" should only change cube face size / partial panorama width, no cutting size. And saving the project after changing those values should permit to reload them exactly as they were saved.
I tried with both 32 and 64 windows versions and it seems to work.
Do you have the krpano registred? Could you save your project under a different name and open this later to check the size?