Programmer not responding - Custom board

[imagiro1]

I've created a custom board based off the R5 USB. It has an Atmega 328p (16Mhz @ 3.3V) + FT231XS. I can program the bootloader (DualOptiboot_V5.0_atmega328_BlinkD9.hex), but I'm unable to program via USB. I always get stk500_getsync(): not in sync error.

Here's what I can is working. I can program the Atmega via programmer (Using Arduino as ISP) and blink the LED on pin 9. If I plug the USB, a new COM port appears (most of the time! Sometimes it says unrecognized device. Makes me think the FTDI IC might be bad). I've checked all solder joints under microscope. Everything looks good.

Things I'm not sure about. Fuses. I've seen different fuses on the forums. I'm not sure which are correct. DTR/RTS. Which should be shorted?

Any hints/ideas? Thanks.