One of Apple's goals with its latest version of OS X is to preserve battery life for portable systems by implementing a number of features which automatically reduce energy usage. These features include App Nap, which tracks the programs and processes you have in the foreground, and "pauses" any which are hidden from view.
For example, if you enable the iTunes visualizer, but then move another window over iTunes so the visualizer is completely covered, then the visualizer will be paused so processing power is not unnecessarily dedicated to keeping it playing while not in view.
While great for battery life, there may be times when App Nap could be undesirable. If you have a program that takes advantage of App Nap, but you'd prefer to leave it running at full capacity at all times, then you can disable App Nap for that particular program.
To do this, locate and select the program file in your Applications folder, and then get information on the file by pressing Command-i, or by choosing Get Info from the File or contextual menus. In the information window that opens, under General, you will see several application options you can enable or disable. These include opening the application in 32-bit mode, opening it in low resolution, locking it, and, for programs that support it, an option to prevent App Nap.
Check that option, and that particular program will no longer "pause" when it's in the background, or minimized.