This is happening to me, too - but it doesn't seem to be limited
to koji notifications. It happens with bugzilla notifications as well.
There isn't any pattern to the delays that I can see.
I regularly receive notification digests during the day,
yet every now and then I receive a digest informing me
of stuff that happened 2 or 3 days ago. I think once
it informed me on stuff that was almost a week old.
My settings in Fedora Notifications are "100 messages or 1 hour".
I don't receive many notifications, so 100% of the time,
the time limit kicks in first; most digests I receive
have single-digit message counts. This applies to the delayed digests
as well - I've never seen one actually reach 100.
A.FI.