Ordinals have always been designed to be applied only to selected text. That said, what I see in your screen cap is definitely strange.
Are you using the same font and version?
The behavior of ordinals depends on the font (to be precise, on how the OpenType feature has been programmed in). Some fonts use "smart" ordinals, reacting only when preceded by a number -- the very smartest ones only set "st" in superscrpt when preceded by a "1". Others always apply superscript, which I believe is what you see here. (Not all characters are superscripted because apparently this font does not contain a superscript "k", for example. Which characters are considered "ordinals" is left at the discretion of the font designer.)
Additionally, it's entirely possible the Ordinal feature behaves different in different versions of InDesign. Adobe is constantly tweaking OpenType behavior. It's extremely likely the behavior in your original version (the very first "CS") was actually incorrect and was fixed somewhere in one of the next five versions.
All said and done: Ordinals is definitely *not* a feature to always have switched on. You should only apply it to text where you would *want* your ordinals, as in your "90th".
Thanks. I didn't change the font (its Adobe Caslon Pro), but I installed CS6 on a new computer, so I suppose its possible that the version of the font that was included on the CS6 disk was newer than the version that was included as part of the older CS (which was on my old computer).
It sounds like the fact that I didn't have problems earlier was just dumb luck. From now on, I'll leave "ordinals" off except for the specific characters where I need that formatting.