It isn't the Abstract, it's the .SH, which calls .RT, which somehow changes
the FS macro. If you replace .SH with .RT in test.ms nothing changes; if you
delete it altogether the missing footnotes appear.

If you put .pm above and below .SH (or .RT) and run:

         ; htmlroff -ms -mhtml test.ms >/dev/null |[2] grep FS

you can see that the FS macro is being messed with. I'll dig further...

umbraticus

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