Hi Phil,
phamousphil we have set the footnote number character style to OpenType Superscript with proportional lining and Document Footnote Options Position to Superscript.
I think that's a redundancy. Set the character style OT superscript, and the footnote position to "apply normal." I don't think that's issue, but it eliminates one thing.
The next thing I'd double-check is whether the font actually has all the digits in its OT superscript proportional lining collections. Sometimes only some digits are available. For instance, does this issue only occur with 7 and 8?
Beyond that, it's hard for me to say without examining the file itself. Feel free to send me the file (or a few pages from it) in a package (with the fonts, I guess, as they may be the root of the problem), and I'll be happy to take a quick look...