Name brand systems tend to come with their software offerings pre-installed. You don't waste a day or two installing and setting up your operating system, drivers and major tools. Tight integration between major components and their associated software means fewer problems up-front. You generally don't have to put up with buggy video card drivers if you buy an Aptiva from IBM, for example. If you really want to drop a system into your office and have it take off running fast, a name brand machine is safer than a standard system.
Quantity purchases Some retail organizations buy in huge volumes directly from the manufacturers.
They tend to specialize in high volume corporate sales. You might be surprised. The inevitable problems All computers, name brand or otherwise, run into software compatibility problems as drivers and operating systems are updated from time to time. If you're still learning, those kinks will cost you time. You will be forced to learn as you resolve them.