Thank you for your reply, Henrik.

I was able to successfully load my program using the U2 programmer and the circuit works correctly, so it's definitely not the programmer, as you suggested.

I didn't mess with the serial connection or change COM port or settings, but I'll check again just to rule it out. I did change the baud rate of the COM port in an attempt to get it working, so maybe that's not consistent; I'll check that too.

Were the steps I took to load the bootloader correct?