Could I get an ssh access on one of your MailCleaner (Optionnally: change the root password before giving it to me via private message) to investigate the case ?
I didn't notice this anomaly and there were more than 900 download of this new Final MailCleaner so I suppose this is a specific problem on both your machine (else i hope people would have invade the forum and would have launch object to developpers ).
If messages are not present in spam quarantine but are present in tracing, this means than the slaves (could be the slave instance part of the master) can't connect to the main instance of the DB to indicate the received spam. Two cases:
1) You also used the Patch to mix 201410 and 2017** and it appears than there is a bug in this patch of you should'nt use it in your case.
2) There is a problem with passwords between main DB instance and slave instance. Nothing known but should have appears in red during configurator or could be related to initial configurator DB bug but can't happen on a final.
I will PM you soon.
By the way; single instance of MC (not clustered).