It could be that the Global Object Styles you have set up in Captivate 6 are using slightly different font size settings for default types of captions and these settings are over-riding your imported project settings for the same objects.
To look at Global Object Styles you need to have NO CPTX file open in Captivate at the time and then go to Edit > Object Styles Manager. Check the font sizes for the types of captions that are being affected and see if editing the global style makes any difference next time you open a project to upgrade it.