Atmega328P-AU is working, but won't take an upload

I burned the boot loader on these, and then uploaded a sketch that blinks D13, and sends a Serial String out every second, so it is easy to test them when installing them on new boards. I uploaded this sketch on them via arduino's boot loader, not the ISCP header, so that I'd know for sure the bootload went ok.
So now, I have two of these new boards, and and after populating them, they both send out the serial string when I connect them with my FTDI breakout, but neither will take an upload. Being that they send out the serial, that means the power supply is connected to the chip correctly thru the FTDI breakout, and that the TX is connected. I check the continuity of the DTR pin, and the 0.1uF cap on it, which checked correctly at 100nF.
Any ideas why this would be. I even took off a few components like a Pololu SW and a remote RF receiver from one of them, but that didn't help.
I've cleaned them 3 times with alcohol and a toothbrush. I've also connected 12v to it's powered supply which feeds the board thru a 5 volt LM1117, and it would light up the onboard LED and continue to send the Serial string...

edit: I'm sorry these photos are upside down! also, I've tried my FTDI cable with a different project, and it works fine loading sketches on it. It's also the Atmega328P-AU version.

Oh, the issue is, I get the message avrdude: stk500_getsync(): not in sync: resp=0x00

photo 2.JPG

board.pdf (43.5 KB)

I figured it out. I had to change to board to Arduino Pro Mini, instead of Uno. On Atmega328P-AU chips I've bought with the boot loader already on them, I just just UNO as the board, but when I loaded the boot loader on mine, I used Pro Mini as the board. The ones I've bought must have had a different boot loader on them.