Unfortunately I'm already using KTE 3.7.0, so it's not a problem with the plugin.
I just discovered that if I use Kobo Utilities' "Update ToC for Selected Books" function to update the ToC on the device, it fixes the issue... Which I suppose is an acceptable workaround, but it does add an extra step I'll need to remember whenever I send sideloaded books... Wish I could figure out what the actual issue is!
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