After a couple of months, I pulled out the boards again and wanted to work on some programming. One of the boards uploaded fine, and the other I was getting errors such as:

avrdude: verification error, first mismatch at byte 0x0042         0x65 != 0x8d
avrdude: verification error; content mismatch
avrdude: verification error; content mismatch

I was also getting another error occasionally with USB device not recognized. Forums suggest that this could be a bootloader issue. 

First I checked the power to make sure that it wasn't a power boost issue. Looking at the schematics I found the right pins to measure.

Since it wasn't a power issue, I pulled out the trusty tag connect and burned the bootloader again. I used the following setup and settings.

Note: At this point you can upload the program through the SPI pins, but it will wipe out the bootloader, so don't do this unless you're not planning to program through serial.

Then I switched to my FTDI programming cable. First couple times, I would consistently get the error message:

Using Programmer : arduino
Overriding Baud Rate : 115200
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 1 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 2 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 3 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 4 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 5 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 6 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 7 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 8 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 9 of 10: not in sync: resp=0x45
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 10 of 10: not in sync: resp=0x45

avrdude done. Thank you.

But trying a few times, once reburning the bootloader, it worked and I was able to upload my program. Hooray! It's not exactly clear why it works sometimes and doesn't other times, but note to self to keep repeating steps with the correct settings and eventually the program will take.