Moved to the appropriate forum
The only answer we can provide is that it is yet another quirk with this antiquated PHPBB 2 software used for the web board. Somethings just happen. A partial answer would be if your able to understand the PHP language, you could see in some of your examples the differences.
A questionmark ? in PHP means GET. So if you see in a link ?t, would indicate GET title, or GET topic. There's some other paths located in your link examples that can completely change what data it retrieves, and how it is displayed. SID is a re-direct.
Finally as to the main subject title of your inquiry, Email being sent by the web board has been hit and miss for a long time. So do not be surprised if you don't get email notifications for posts, PMs, or if and when you do, the links contained in them may not be correct.
Ron Petersen, Web Board Administrator