Hi Ulodesk
I have just redone it, made sure I definitely selected formatted text (I had to because of the superscript, so I must have done before also), and I still have the same effect.
I have only chosen one shortcut in both cases, which is 99mTc or 123I, however, if I try to add a different capitalisation to Proofing, it automatically selects the current one in the list, implying to me that I capitalisation doesn't influence the shortcut. Yet typing the shortcut in the document without a capital (at any place, doesn't have to be the same place as the original shortcut) doesn't work.
It's largely through lazy typing that I am trying to fix this, ironic considering I am typing more here than I would have to press Shift in my document

But it's also curiosity as well now.