the digits look completely regular.
The above phrase makes me think of two possibilities: a) digits in your text are shown with some other font or b) your custom font contains the second set of digits. Are you sure your text contains usual figures named from "one" to "zero"? Is it possible that some alternative set of figures (e.g. old style) was selected?
The more simple cause is that the font was cached by InDesign and still shows the previous version. This usually happens on Mac OS X. You should simply reset font caches in this case.