I am a long time user of SpamSieve. When I upgraded to Yosemite, I noticed a slowness in flagging messages with SpamSieve, both spam and good ones incorrectly classified. Strangely enough, things got worst when I bought a new MBPRo 13" in June. And the situation became hopeless when I upgraded to El Capitan. Now I get beachballed whenever I try to flag a message. Things eventually get resolved after a few minutes. Sometimes not.
I include two samples, one for Mail and another for SS, taken by Activity Monitor during one of those tantrums induced by my flagging a message as spam. The same problem occurs when I try to correct a wrongly classified message in the spam folder.
Hope you can find a solution.
Sample of SpamSieve.txt (274 KB)
Sample of Mail.txt (515 KB)