What kind of case is this? Are you certain the connectors are matched correctly to the headers on the board (2.0, 3.0)? PIN configuration matters as well. Some cases have plugs where the PINS in the plug don't match the header on the board. <<< USB 2.0... 3.0 always matches.
Do you ever see an error in the System Tray.. This USB Device Could Perform Faster....
What does Device Manager show? Any issues there. Do you hear the detection sound when a device is connected? Is it dropping off during a large file transfer??
The bus should be robust enough to handle multiple simultaneous connections. However, if the PIN configuration, connection or power draw of a device (example) is high, it could cause other ports to drop off unexpectedly. Using powered/unpowerd hubs can cause issues too.
