Thanks for bringing this to my attention Husse and I also agree with what cmost said (I usually do actually
Before I try to explain anything, I also think there's a bug somewhere as a manual refresh sometimes brings updates that are not brought by automatic refreshes.
Now, on to the explanation of why, to some extend, mintUpdate cannot know about these updates in some particular conditions
--> When you log in Gnome, mintUpdate is started with your user rights... it sits in the system tray and refreshes itself every x minutes.. but it doesn't have root permissions so although it can see what packages are available, it can't perform an apt update... so it could be sitting there for 4 days and never see updates until another program with root permission performs an apt update.
--> When you click on the mintUpdate systray icon here's what happens: a new mintUpdate is started as root (that's why you see a gksu dialog asking you for a password) and the first thing it does is to kill the older mintUpdate (which was running with user permissions). So you're now looking at a mintUpdate with root-permission and from there on, it still refreshes every x minutes... but this time it's powerful enough to perform apt update. Here's the dirty hack
Anyway, basically remember that until you click on mintUpdate and input a password, it can't do apt update... and the minute you open it, after that it can.
--> Now, the bug I'm suspecting is that when you open mintUpdate as root (click on it in systray just after logging in Gnome).. it doesn't look, at that precise moment, like it's doing an apt update... because if you actually click the refresh button you see more updates than it initially came with...
Let's tackle this anyway and if there's anything else please report the names of the particular updates it sees and doesn't see and in which conditions. The key for me to be able to fix a bug is to easily reproduce it, from there on it's a very simple matter.