@jaaakee: The first thing that comes to my mind is "compability".
I've heard several times people saying that certain applications run "better" or only run at specific browsers.
The reason for that is the code they created to execute something, in our case the codes, probably runs more efficiently on certain browsers.
Maybe the most recent browsers have capabilites to support our applications, that each day require more and more things to be done.
I once tested Codecademy on IE and I have to say the page took quite a while to load, where on Chrome it loads almost automatically.
Could it be an extension, a malware or something? Maybe but I've checked and there are no such things.
The user who's been complaining about the fact the message was not being prompted could check if he/she didn't mark a checkbox saying if he/she didn't want those messages to show up on their screen, which we have to agree is relatively annoying at certain times.