The font is in the correct (an order) in the glyphs window in Indesign.

In the contact sheet the accented glyphs seem to be in order, it's just the upper and lowercase that aren't in the correct order.

The font is in the correct (an order) in the glyphs window in Indesign.

You sure about that? You can change the sort order in the Glyphs panel, so possibly what you see is with the sort order is set to "Unicode". Make sure it's set to "Glyphs".

The 'correct' order being ascending Unicode value, I presume. Glyph IDs are assigned in the order glyphs are added to the font, as far as I can tell.

I know there is no correct order as such.

OK so the order in the contact sheet is the CID /GID order in the Glyphs window in Indesign.

I want the order in the contact sheet to be the Unicode order.

The script you linked to does not work that way. It only writes out glyphs, unaware of the associated Unicodes -- if any! As it happily outputs glyphs with no Unicode as well; it was written for exactly that purpose.

To get an output sorted on Unicode, you need to know which glyph in the font has which UC associated with it. Re-associating the glyphs with their Unicode code points is no easy task: it requires reading, parsing, and sorting the cmap entry in the original font file, all in Javascript.

In FontLab, you can control the order when you're in the Font view (the main window, showing all the glyphs). Choose "Sort Glyphs > By Unicode" from the Glyph menu. You can also fine tune the order in the Index view of the Font window by dragging glyphs around.