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After messing around with the profile for a while I noticed that storage.sqlite in the profile directory was empty compared to a profile with a working stylish install. I copied the non-empty version to the broken install, and it worked.
To replicate this bug just delete storage.sqlite. It is replaced with a file that is 0kb
Could Stylish be forgetting to check this database is not empty before trying to read it?
Also clicking Ok on that box does nothing.
Additionally, going back to Quantum does not fix the problem.
I can provide a (clean) zipped copy of the profile with storage.sqlite missing, replicating my issue. It contains a working copy of storage.slqite.
Oh, and my version of ESR is 52.6.0 (64-bit)