Custom arduino, fails to sync instantly on reset.

Hey! So I have a custom atmega328 arduino on a board which was working fine, but I decided to clean up the wiring, and making the 2 halves of my robot easier to seperate and plug back together.
But I can no longer upload through the same serial module. When I try to upload, the arduino resets as normal, but then resets again, and all 10 sync attempts fail at once with a 0x00 error, rather than trying to sync again after a bit of time. Any ideas what this could mean and what’s going on? My arduino has it’s own power supply as well (as well as a few backup caps), so I’ve confirmed it’s not due to a brown-out/voltage sag causing the additional reset.

Here’s a video:

I have double-checked the wiring between the MPU and the serial connector and the serial monitor is reading the arduino fine.
All I can think of is that there’s now a lot more wire between them (since they are no longer directly connected, but going through a data connector I custom made), could that be the cause? If that’s the case, how to I make it work with longer wires?

If the ribbon cable connects your arduino module and serial module, then it is too long. When you open serial port and confirm that arduino and PC are talking, what baud rate did you use? The upload baud rate is 115200.

Yeah, my serial adapter is through some wires, to the ribbon cable, then from the other end of the ribbon cable through some more wires that finally reaches the Arduino module.

I use 9600 for the serial monitor.

I also realized another difference since last I uploaded, I added an antenna which uses SCK, MISO and MOSI.

Then antenna shouldn't matter. Those SPI pins weren't used in bootloader firmware upload. The reason you CAN use serial port was because of the low baud rate at 9600. I'm not saying you can stretch a hodge podge of long cable at 9600 rate but it works with the cable you have, say 50cm or 1.5ft long, but the look of it. I found it myself that longer wires at higher baud rates don't work. Using Arduino Nano's bootloader drops the upload baud rate to 57600 but probably won't solve your problem. Think about how to shorten that cable, or hook up to SPI pins and use another arduino to program your robot, if by doing that you end up with short cable on SPI.