I'm wondering if anyone can explain what's going on here and possibly find a solution. It's a little hard to explain so I'll just start by explaining how to reproduce the problem.
Don't forget to put a 10uF capacitor between GND and RESET on the UNO that you're plugging in to your computer (the bottom one in the diagram on that page). Follow steps 1-7 and burn the bootloader.
After successfully burning the bootloader, open the Blink example sketch and select "Upload using Programmer." The little LED for pin 13 should be blinking away nicely.
Now, unplug both UNOs and set aside the one you were just using as an ISP. Plug the UNO with the newly bootloaded ATmega328P into your computer and try to upload the Blink sketch again. The upload will fail, saying that the programmer is not responding.
Does anyone know why this is? If you burn the bootloader using the ISP but don't upload any sketch using the ISP, you can upload sketches to it directly with no problem.
Sorry if any of this is too confusing, I've spent a good 3 hours troubleshooting my connections here and I'm a bit tired. If you need clarification on anything just let me know.
If you uploaded blink using "Upload With Programmer", it will have erased the bootloader.
You will need to re burn the bootloader using ArduinoISP in order to upload normally (via usb).
CrossRoads:
If you had two arduinos as pictured above, why not just connect USB cable to the 2nd Uno & download sketch directly?
The two-arduino setup was just me troubleshooting. I initially noticed the problem when I used my ArduinoISP shield to burn the bootloader and upload a sketch to an ATmega328P. After doing that and putting the ATmega328P back into an UNO I couldn't upload any more sketches to it, so I wanted to verify that this wasn't a problem with my shield.
You may have a mismatch in speeds between what the bootloader is using and what the IDE/PC is using.
I had the same problem a while back - had loaded optiloader on a chip I had on a Duemilanove - if Duemilanove was selected as Board type sketch downloads failed. Sketch download did not work until Board type was selected as Uno.