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I have had similar problems in two cases. The first isn't relevant, because you are not seeing messages about killtimers. The second is, I think. I have seen problems caused by bad fonts.
The message "tt_face_build_cmaps: broken cmap sub-table ignored!" indicates that you have a truetype font installed that contains an invalid character mapping table. Calibre is discovering this font during font enumeration, but unfortunately the message is printed by the truetype library, and (as we see) it does not tell us *which* font. My impression is that once the font enumerator runs into a bad font, it never properly recovers.
I see from your fonts.txt that you have a lot of extra .ttf fonts installed. Unfortunately, one or more of these is probably bad. The 'right' approach is to restore the windows font directory to its original set, then add fonts back until you find the one that is broken. Another approach is to create a VM with a clean Windows install. Both have their drawbacks.
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