Can burn bootloader but cant upload code

Not quite, I believe that my bootloader burn was successful as now it operated without a crystal. However I cannot upload code to the board even if I don't touch any wiring. I haven't tried Rx/tx recently but the last time it was not successful. I think that I am under a false impression that the bootloader has burned, as I dont have any very solid evidence as I can't upload code to test. When given power the custom board gives high pulses on the clock pin. It refused to do this until a crystal was in place but after the bootloader was burnt it would keep going without the crystal. Sorry if that's a lot but I don't understand how the bootloader was successful and yet it doesn't allow for me to upload with the same wiring configuration if it's communicated with the chip