Recently, I encountered a strange bug. I was working on an IntentService responsible for notifying the user upon receiving an intent; among other things it could do was update a notification about something in progress. It looked fine in most cases, but I discovered that if it was being updated while a "Looking For GPS" or keyboard selector notification was also up, it would 'flash' on each update - disappear and reappear redrawn.
I have yet to delve into the Android code to understand the disparity, but the solution was straightforward -the IntentService was building an entirely new Notification each time instead of re-using the same builder/notification to generate it.
The takeaway: if you plan to have an ongoing notification, it seems you'll need to hold on to that notification/builder object so you can notify the NotificationManager with it in order to prevent flashing.