It seems you are using a variation of my comments-in-output code from Notebook formatting - easier descriptions for equations and results? The variation you are using does not actually produce any formal output; it merely prints the evaluated form as a side-effect. Despite its name $PrePrint does not affect the lines produced by Print, as these are not considered output.
You can either add ScientificForm and PowerExpand to your modified $PreRead function:
$PreRead = Replace[#,
RowBox[{body__, ";", note_String?(StringMatchQ[#, "\"*\""] &)}] :>
Print[ScientificForm @ PowerExpand @ ToExpression@RowBox@{body}, Spacer[50],
Style[ToExpression@note, Italic, Red]]] &;
Or as I would prefer you can add it to my original code:
$note = Null;
$PreRead =
Replace[#,
RowBox[{body__, ";", note_String?(StringMatchQ[#, "\"*\""] &)}] :>
($note = Style[ToExpression@note, Italic, Red]; RowBox[{body}])
] &;
$PrePrint =
If[$note =!= Null,
# &[Row[{Pane@#, Spacer[50], $note}], $note = Null],
#
] & @ ScientificForm @ PowerExpand @ # &;