There are occasions when FAH will hinder other running programs

From FaHWiki

Once upon a time, the distributed computing world was populated with tiny work units and easy calculations. This is changing as computing power in the personal computer increases. With the additional processing power available, many DC projects are taking advantage of that power. Work unit sizes are increasing and system requirements with them.

The Folding@home project has kept its original design goals for a DC client that only uses spare CPU cycles, and has little performance impact on the computer. One example is the ability to reduce the total memory available to the client, configurable in the client setup. But F@h has also taken steps to harness that growing PC power by enabling preference settings for downloading large work units, or requesting advanced work units. And these advanced features will impact system performance to varying degrees.

And the new High Performance F@h clients, GPU and SMP, are designed to use maximum resources, and will definitely impact the performance of other applications.

Please take time to study how setting changes in the client can affect performance: