usb shields connectivity very delicate?

I'm having some issues where I have to hit reset and toggle the digi inputs to get my arduino to communicate with a USB device that I'm controlling.

Could there be a problem with my Arduino's boot? Could it be my code?

The (default) Arduino USB port is a serial slave device, that can be connected only to an USB master. Connecting to another USB slave requires to turn the Arduino USB port into a master. For that purpose the USB firmware must be flashed as required.