After a discussion started by Richard Hughes on the mailing list and in his blog I have got at least 6 different requests for having the tray icon new item count display as an optional feature (or not at all). While I would have preferred for some of those wishing to have this choice to supply a patch I ended up doing it myself.
This is the new notification preference option group:
The default setting for the new count display will be disabled. So if you do want to use the feature which was on per default in 1.2.7 please take the time to switch it on.
If you are familiar with the preferences you will notice the second new preference "Terminate instead of minimizing..." which solves another problem with the tray icon usability. Among different applications and interface guides there are quite different opinions for the right behaviour of an application with a tray icon when the last window is closed.
This option which is disabled per default (matching the behaviour of older releases) allows you to configure this behaviour.
Last but not least the question about the usability of these configuration flags. From the usability standpoint I think they are definitively too much options, but due to the non-standardized behaviour of tray icons there is no better way than to let the user decide or to enforce the developers view. In this case there is so much negative feedback that I fear the options are justified.
To be released with 1.2.9