Counters and sound cannot be disabled

No, it's not a known issue, but it may be a case of bad GUI design. The four buttons to the left illustrate positions within the dock icon. It was a quick hack in its time, but it has never been improved (and it's not a high priority). Make sure you have disabled checkmarks and sound for all 4 counters.

Does this explain what you see?

I see. I thought it was the position of the counter, not that one could configure four of them. Maybe some text there could help, or a tabbed window (with "top-left", and so on as names, and using the place of the four radio buttons to put a preview).

In any case, you can file this as "not a bug". Thanks.

Yeah, this is not a bug, but it confused me too. This definitely should receive some GUI polishing. Arbitrary colors would be appreciated as well.

Arbitrary colors are actually supported, but there is no GUI for it:

defaults read com.freron.MailMate MmCounters

You might need a property list editor to change those values (included
with Xcode).

As a new MailMate User I can confirm that this is very confusing, since the radioboxes suggest you only set the position of the Dock Icon. It would be much better to use Tabs here or so, or at least explain it better in the Help section. Took me forever to find this "Bug" report here, which finally helped me to discover how this works.

@Marvin: I've added an emphasized note to the manual and I've changed the positions of default counters such that the main one is to the top right and this is selected by default in the preferences pane. Eventually I'll completely change how counters are configured, but hopefully these changes can be an improvement for now.