SpamSieve keeps erasing emails, instead of moving to Spam folder or leaving in Inbox

I really want to love SpamSieve, however, I have one serious issue with its reliability.

I receive emails on my iPhone and on my Mac (OS X 10.10.5) using the Mail app.
Since SpamSieve runs on the Mac which only checks the Exchange server periodically, I see emails on the iPhone first.
When the Mac pulls the emails from the server, SpamSieve filters them according to the rules and the spam emails disappear from the Inbox on both iPhone and Mail app.

So far, so good!

However, intermittently I catch SpamSieve completely erasing certain emails, not following any particular pattern or sender; they cannot be found anywhere, neither in the Inbox, Spam folder, and don’t even show up in a Spotlight search.
I took screenshots of the emails on the iPhone and once SpamSieve eats them, they’re gone.
I contacted C-Command Support several times without any response.

Please help!
I have lost important emails this way and without being able to trust SpamSieve 100%, it cannot be relied upon for business email!

There’s probably something else going on here, because SpamSieve does not delete any messages (even suspected spams). Please see this page for more information.

I don’t think your messages ever arrived. I reply to every support request. There have not been any recent ones about this type of problem. And I searched our complete e-mail history for the last few years, including spam, and did not find any from the address that you used with this forum post.

The poster contacted me via private forum message. It turns out that he had e-mailed in early February using a different address, and I had replied, but he did not receive the replies.

Awesome!

Thank you very much, Michael, for working with me to get this problem resolved.

The bottom line is, disable all other mail rules as well as the junk filter, which seemed to have been the problem in my case, and let SpamSieve do all the work!
It seems to be working perfectly for me now.

So nice to hear (or actually see) a happy ending!