I'm getting this exact error after launching a site using 2.6.1 for the first time.
I ran the site through Xenu link checker to try and trigger the error message, but it ran fine, suggesting to me that the problem doesn't lie in the site templates.
The System Notifications module appears to create a table in the database called field_notifications, which holds the data that is used for the notifications.
It would appear that the error is being caused by a 404 error trying to be added to this table without a unique pages_id and sort. 41 is the superuser ID I believe. So essentially what is happening is the system is trying to add another record (pages_id = 41, sort = 0) when it already exists. However, I can't seem to replicate this however many times I generate a 404!
Any ideas what might be generating the 404 that is causing the error?
(PS - Going to disable the 404 notifications for the time being)