I initially had fingerprint scanning working with just one finger; after I had tried to enroll several more fingerprints two weeks ago, I was unable to get the fingerprint scan prompt (and instead would just have to enter my password for root operations). Following your observation, I just tried clearing my fingerprints and only enrolling three fingerprints, and now fingerprint scanning seems to work again!
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Interesting, not something I have tried. Never occurred to me to enroll more than three. Could be worth clearing the prints and trying again. Assuming this is a single boot machine, of course.
Funny thing is, I noticed this after clearing the fingerprints a few times while I was troubleshooting using the AppImage mentioned here. I remember after I cleared them the first time, it had the same issues after setting up 4 fingers, but after clearing and setting only 3, things worked.
Also, yes, this is a single-boot machine running Fedora 39. Can confirm, no issues since I set things up earlier!