All dots are invisible after repackaging a font, only in Illustrator.

Yesterday I repackaged a set of loose fonts into the same family with the help of Robofont and this tutorial.

Now if I use the font in regular in Illustrator, the dots in characters like i, !, ? and j do not appear. When I switch to italic, the dots are back. This only happens in Illustrator, in other apps, the dots show up fine.

Looks to me that somewhere in the repackaging things went wrong. I just can't understand why it would only happen to the non-italic fonts, and only in Illustrator.

Has anyone else ever seen this issue? Ways to prevent it?