Works with boot loader but not without

Hello All, i have an issue with a new feature i'm adding to an existing product.

basically i have a MIDI controller that i want to be able to "Teach" new commands. the project that this is for already exists and so my pin configuration is set. in order to teach a new command i need to make the TX pin a software serial RX pin. this works fine on my Arduino but when i tried it on a 328 without the boot loader something went wrong and the command read is not the one sent. i think this is either due to a bit being missed or clocking issues. i really don't want to have to use the boot loader, can anyone think of what might be causing my issues. ?

Ps. sorry for not including any code. its very long and i'm not sure what is relevant.

Do you have a crystal or resonator providing an external clock signal to your "328 without the boot loader"?

What baud rate are you using for the software serial communication?

hi. the clock is internal 1Mhz and the baud rate is 31250 (midi)

robparkie123:
hi. the clock is internal 1Mhz and the baud rate is 31250 (midi)

And so have you burned the fuses for the correct clock speed?

sorry for the long delay in answering

yes i belive so. sending midi works fine in another area of the code the only bit that is not working is reading midi correctly.