Do you know if the bit bang pins default to inputs or outputs (or if the mode persists through power loss)? It could be a problem if you had to explicitly set the bit bang pin used for reset to an input every time you powered up the board. Also, reading through the documentation, it wasn't clear to me which function actually set the states of the bit bang pins (I didn't spend much time on it); do you know?
The pins can be set to bit-bang mode through the FTDI programming tool. It needs to be burned once into eeprom only once through the programming tool.
See MPROG from http://www.ftdichip.com/Resources/Utilities.htm