This is NOT very elegant, but try a new document to see if you still have this problem

"Trash" can sneak into a document, so at times, to save time, just do a new document

If a new document works, then Copy and Paste Special > Unformatted Text into the document that works what you have in your bad document

(You want Unformatted Text to be pasted, because you do NOT want to copy any trash from a bad document)

Failing this, then look into the following:

Do you see any difference when you compare what you see when you:

Insert > Symbols > Equation > [Equation entered] > then under Equation Tools > Design > Tools > Downward Arrow in the group > Equation Options to spot any issues