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Yashinon,
Almost certainly, the explanation lies in the difference between two font series : the “classical” one, where the proper numeric parts of a chemical formula are expressed as genuine subscripts (and generally even superscripts – remind ions) and new Unicode fonts (Arial Unicode or Calibri), where subscript and superscripts are also autonomous characters. So in your second case, the notation in a cell is correct with proper subscripts that, however, are not inherently displayed in the scripting row.
In the first case, the record in the cell was created by means of subscript characters that, on the
contrary to the previous situation, stay as such when displayed; the last 2 is left in basic size. This method has a main advantage in the possibility of referencing the formulas without destroying the proper layout of subscripts. The main drawback is in very poor availability of subscripts, and superscripts greater then 3. These characters are coded with number 8320 and followings, so picking them all up is difficult for an outsider. The reference of a chemical formula with formatted subscript, of course, doesn’t respect any formatting of individual characters, and so the reference cannot be formatted independently.
You can prove this explanation by checking up the different fonts in dissimilarly behaving cells.
All that labor can be largely facilitated by a series of user defined procedures (macros) hinted in the basic version by Rick.
Regards
PB