Quit the app and open the folder /Users//Library/Application Support/SpamSieve/. Inside there should be a folder called Log.spamsieve-logd. Try renaming this to OldLog.spamsieve-logd. SpamSieve will start a new log database without all the old imported data, which is not needed for filtering accuracy.
Those changes made startup pretty much like any other app, so those worked. And it improved processing performance, but not nearly enough - I got one email processed in about 5 minutes, and SpamSieve kept going into unresponsive in Activity Monitor. So I took a sample about a minute or two in, hope that helps. Now the cycle time to turn on/off is less than 5 minutes so its testable now
With your latest sample, the main source of the slowness seems to be reading the corpus database during filtering. This is an area where an SSD makes a huge difference. Since your Mac has tons of RAM, though, it may help to increase the memory cache size, which you can do by clicking this link.
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