It looks like you currently have no filtering happening because you’ve told SpamSieve to use the plug-in setup but not set up Mail to use the plug-in. Because you were getting plug-in related errors before, I would go back to using Enable spam filtering using Mail extension.
I’m not sure the defragmentation really worked. The Words database file is still broken into 32,279 fragments. Maybe there wasn’t enough contiguous free space on your drive.
That said, this sample is very different. It no longer looks like SpamSieve is busy reading the corpus. Rather, Mail is getting bogged down and reporting timeout errors, and so SpamSieve is giving up waiting for it. In this particular sample, an error is being reported to SpamSieve, and it’s stuck waiting for macOS to gather information about the error. I’ve not seen that before, but I’ll send you a test version that tries to work around that problem.
I had thought that 3.2 broke, but you informed me that things went bad on my system prior to that update. No idea why things went south.
Just as mysteriously, SS is now again working (almost) perfectly! I still see a few timeout errors in the log, but subjectively, I’m no longer experiencing any hangs or delays. When spam is auto-filtered, it no longer remains (brown) in the inbox for 10 seconds before disappearing.
I haven’t changed anything on the system. No new installs, extensions, etc. No OS updates. Nor have I changed any settings in Apple Mail or SS.