Do you have other things connected to the Tx/Rx lines also? If so you should consider a way allow them to be disconnected so the rest of your circuit does not interfere with the FTDI (or similar) output during reprogramming if you're going to have it soldered in place. Other pins may be needed also. I have a promini that is on a socket in a board with some other logic chips which the promini drives. I have a jumper between the Rx in and the buffer that I bring serial data in on, figured I'd be all set - and yet no, have to pull the promini to program it. Have not figured out where the interference is coming from, kind of a pain to disconnect wires one by one to chase it with everything all neatly wirewrapped. I've got something on every pin, even the inboard A18/A19 have square pins with a jumper going to the board. All are outputs except for the data output from the RF module, guess I can try pulling that one and see if it does it. In the meantime, I am pulling the promini to program it and just concentrating on getting the software functionality done as the hardware is all working.
Could be the 5V on the VIN pin even for all I know.