Since I have Mathematica 10 I note this trouble
It is worth noting that the various characters used in typesetting of formulae come from specific fonts that are shipped with Mathematica rather than from standard system fonts. So, it is my guess that the only things that get applied to the inline cell formula fonts when you change the cell's font , are particular aspects of that font change: e.g., FontSize, FontWeight, and so on, but not the font itself.
Thank you, you help me a lot to understand the trouble : the appearance of special ans Greek Character depends only on the font used.
Example of different shapes associated to différent fonts
I have many pages written with a lot of formulas, all the proofs are styled with my handwrite-font which is associated to a wrong shape.
I don't want to change the font, and I can't change the font for each character.
I'm looking for an option with which we can force the shape of special and greek characters
You can select the inline cell (the formula) itself and apply a particular font to it.