A lot of the aftermarket mufflers like Slimline and Jtec are really more like exhaust diverters. People use them to get the exhaust to a more scale like or convenient position. R8893 is correct about needing some back pressure for the fuel system. A lot of the issue depends on the specific muffler that you are using. Some of these mufflers are designed to mate to a specific engine and probably work well in that application. Other mufflers, especially some of the older designs, are made to fit a range of engines. You may have ended up with a muffler that has a lot more exhaust area than the stock muffler for your engine, even to the point of being an open exhaust. For example, you may have a pitts style muffler where both of the tubes have an exhaust area that together are equal to much more than the original muffler. In that case plugging a tube or reducing area can make a difference. It's a balancing act. The best outcome is to end up with a muffler that has about the same flow and back pressure as the stock muffler. Pressure tap location also has an impact. The pressure in a muffler is not the same in all areas. If you look at a stock muffler you will see that the tap is usually located in the area of greatest volume inside the muffler. One muffler that I had, that was not much more than a cube with an angled exhaust tube coming out, worked best with the nipple placed so that the opening looked right down the engines exhaust port. I don't say this to be down on Slimline, JTec or other mfg.s When used effectively they do a great job of getting the exhaust where you want it. It's just that you may have to modify or tune to get the desired performance and reliability.
Your mileage may vary but that's my two cents worth.