I assume you get those notifications in Pebble, not my app?
First, Pebble's own app, as far as I understand, gets triggered by any notifications posted by Aqua -- including those ongoing "Synchronizing with <account>" ones, which do *not* represent a new message.
Second, I guess they are doing their own counting of those notifications, and *assume* that they can somehow figure the count of new messages from that. Well, Aqua can update an existing status bar notification in some cases, let's say there were 4 unread messages, and on next mail check there are two.
Third, Aqua can and will post per-account notifications. A third party app won't be able to connect them to accounts, or to know that they represent two unrelated message counts (which should be added together, if a single value is desired).
To summarize, even though many apps do it, monitoring another app's notifications and trying to make conclusions about what they represent is a road to nowhere. It's just plain wrong.
Some thoughts:
- You can turn off Aqua's "status bar icon" setting under "look and feel" to get rid of those "ongoing" notifications that I guess cause Pebble's app to become confused.
- There was recent interest from the developer of an unofficial Pebble app to integrate with Aqua. I'm very excited, hope it works out.