Are the Input Channels Isolated from Each Other?

No. All inputs on every product share a common ground internally, and that ground is also shared with the USB connection, and thus the host PC.

For more information about isolation, please see this article below.

For digital channel-to-channel isolation, we suggest considering this eval kit from SI Labs: http://www.digikey.com/product-detail/en/SI84XXISO-KIT/336-1765-ND/2170672