I'm experiencing some weirdness with the superscripting of footnote numbers within the text (not in the footnote itself) in book documents that were originally imported from MS Word.
I first noticed that when I went to Footnote Options and chose "Apply Superscript" under "Footnote Reference Number in Text" that it didn't do anything. The footnote reference numbers weren't affected. So I tried an experiment wherein I created a character style called "red" and chose that option.
It worked. The footnote reference numbers turned red and also became superscripted. Then I went back into options and removed the red character style, but the superscript formatting "stuck." So for a couple of the book documents that were giving me trouble with superscripted numbers, I used this new "trick" to get the numbers superscripted.
Only problem is, it's erratic. I was just reviewing comments on a PDF of the first proof when I realized that the PDF had superscripted numbers but my Indesign file had reverted to non-superscripted.
Anyone else have issues with this, or have any idea what is going on? Latest version of ID CC 2015 on Mac OS 10.11.4.
Replying to my own question as a year later I still have this issue. Here is another outline of what is happening:
How can I get footnote reference numbers to work correctly, from the start?
I am experiencing this problem too in ID CS6 on Windows 10. However, your solution does not work for me.
Superscript has two features: (1) reduction of font size and (2) raising from the baseline. When the superscript character style is applied to my notes I get (1) but not (2).
My solution is to recreate superscript manually i.e. specifying a smaller text size and a baseline shift.
In EDIT > PREFERENCES > ADVANCED TYPE the sub and superscript and small caps reductions are specified.