It's less the height of the roof that makes it an ideal mounting location than the fact that you have that nice broad surface all around the antenna to help scoop up the broadcast signals and reflect them nicely so the antenna will pick them up. since there is nothing in the way of the roofline to block the signals it works better than the trunk, where the rear window and "C" pillars obscure a good portion of the signal. Sure the height of the roof helps, but it's more the fact that you've got an unobscured "view" of the radio waves that are bouncing around the car, hitting that wide-open ground plane of the roof. To that end, is there anything on your roof that might be obscuring the antenna? Any roof racks or lightbars(?!?!) or anything like that?
If you are taking the mag mount inside and plopping it on your coffee table or somewhere similar you can absolutely expect to hear a degridation in signal quality indoors. the mount needs a groundplane, and it ought to be metallic to work best. Tables, chairs, magazine stacks, window casements are not going to offer the same ideal surface that your smooth car roof will, and your reception will suffer because of it.
I really would take a serious look at the coax you have connected to your mag mount. I will bet you a doughnut it's something pretty thin and pretty high-loss, like RG-58 or the like. Also, make sure you do not have any kinks in the cable!! Coax is a lot like a garden hose in that respect, and if the cable is bent or coiled too tightly, the radio waves will not flow through to your scanner. Further, bundling it too tightly could crack the inner element, in essence breaking the conduit through which the signal must pass. If you have surplus cord, try making a set of not-too-small loops, like a cowboy's laso, maybe no smaller than a foot in diameter, and see if that makes a difference. Whatever you do, don't pack excess coax the way you see power cords wrapped in a new package, in tight little bundles that are tied tightly together.
Lots of people have been pretty happy with that Larsen tri-band ("I know, that's why I bought it.) What is your budget? Where did you get the mag mount, or was it ordered with the antenna? Check the jacket of the coax. tehre should be printing on it that will say what kind of cable you have. With that information, look up the cable's attentuation details online and see if the stuff is any good for the frequencies you want to draw in. If you have a radio shop or know someone who's knowledgeable, perhaps you could test the cable to see if it is sending full strength signals from one end to the other, or if it is damaged internally and thus "spilling" some signal inside, before the radio waves get a chance to make it to your scanner.
Be safe, have fun.
