Problems with Superscript

I'm having an issue with superscripts. This is an issue with footnoting primarily. For some reason, sometimes when I set a superscript to a footnote, the font ends up much smaller than other times. Take a look at the attached screen captures. The superscript footnotes in the block of text to the left look correct but in the headlines to the right, the superscripted numbers are much smaller. Does any one have any ideas what might be causing this? I've also included the Story file. I'm using the font, Effra, in the whole course.