Re-Fry a PDF to embed fonts

Posted in Acrobat forum, but I think this group is pretty on the ball, and faster.
Received a 6 page file, customer requested we run plates. My normal quick checks; Properties, check fonts, most were not embedded. Run a preflight, all images were below 100ppi. Informed customer, a print shop, to send it back, use a correct options set. Received a replacement file, exactly the same low res, no embed. When they cannot get it right after trying, I normally fix it myself.
Not to long ago, I would have placed the pdf’s into InDesign and exported a pdf with fonts; easy, squeezy, lemon peezy as the commercial goes. But, as I try to use the "correct" tools for the job these days, not pound a screw with a hammer, I utilized Acrobats Preflight > Fixups > Embed fonts. Analyze & Fix. Done, fonts embedded. Place the fixed file, RIP plates.
Got the call - fonts crammed, mostly instances of Times New Roman lower case ff.
I’ve built a visual of the Source PDF (small section) original file, without fonts, Acrobat’s "Fixed" file, and an InDesign Export of the original, sans font, file.
Any idea why Acrobat messed this up? I have done the InDesign place and export on two different machines with identical, good results btw. (Not sure about image size, open image in new tab shows large)
Acrobat 9 Pro, Vista PC

The original pdf's properties showed the document was created with Pagmeker 6.0. I actually cannot recal how PM went to pdf...subsequently imposed by my client via Quite Imposing.
No firm advice from the Acrobat forum as of yet.
It's just frustrating when, in the course of trying to use the "proper tools", a problem without a solution causes the loss of a few hours.

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