Serial Port problems

I tested it with Blink, and the Arduino worked. However, the Arduino Uno only worked when I had no other wires connected to it, besides the USB. Once I hooked it up as in the setup I gave in a previous post...Arduino Examples RD02 Motor Controller serial , then, the Uno would not respond to any changes I made in the blink program (i.e., changing from 3 seconds to 5 seconds). When I would upload another program, the Uno's various LED's would blink rapidly for 1 or 2 seconds, acknowledging that it was receiving new instructions, but then it would just blink the LED to the last uploaded interval that I had uploaded (when it was connected to nothing but the USB). It seems like it won't take any new instructions unless it is connected to only the USB cable. How do I get it to accept new programs?