Released v0.9.7, which employs some black magic to make autorefresh behave when combined with overlay or backgroundless

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That said, I couldn't reproduce any kind of issue with autorefresh, even on the Forma...
But, I've tweaked a few things in 0.9.7, so, who knows...
Do check the
updated default config.
In particular, I've added a link to a NickelMenu config to dump the logs manually, as well as another native option that'll do the same. It only dumps the log when the config is reloaded though, which makes it a bit clunky to use if the only way you can modify the config is over USBMS (i.e., it means a first USBMS session to flip the switch, then another to actually get at the log).
@Carmelocotonto: Since you mentioned KOReader, one interesting data point would be to check if you actually see the clock ticking in KOReader's own USBMS tool... (as it's basically the same piece of code).