Yes, they are part of the games, if you can't see them for some reason, then that's very strange. What you should do is update your graphics card drivers, and then check, and if it doesn't work, then try reinstalling the game.
When you are scanning for quests the red dots are non-scenario quest givers. If you are not seeing any red dots when you scan then you probably don't have anymore quests available to get in that area.
thats gonna be annoying, really strange, reinstalling is the only thing i can think of that might help. has it always been like this or has it just recently started? also, have you changed anything in your game folder recently or changed anything on your computer that could be linked to it malfunctioning?
interesting, to me it looks like T is set to open your map as well as M, maybe if you go into game options and change the settings for scouter? also, try opening your character equips by hitting C and right clicking on your scouter and then clicking on 2, maybe the keystrokes arent right. its worth a shot