Acrobat Fixup Embed Fonts botched it up

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.
Acrobat 9 Pro, Vista PC

Editting the embed fonts fixup does not appear to allow full embedding, but rather only subsetting.
I'm able to recreate consistant flawed results.
I'd appreciate if someone would try to duplicate this flaw. I've hosted a single page of the file at acrobat.com
https://acrobat.com/#d=D39tTXyUXU8sj0plc93jzg
Run Fixup > Embed fonts, among the tracking changing, the word difficult, second line under photo obviously overlaps the ff, two lines below that, offer becomes of fer.

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    Posted in Acrobat forum, but I think this group is pretty on the ball, and faster.
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