In reviewing the design I noticed that by dual-purposing two of the pins on the ICSP connector (SCK & MISO) there is a potential for problems when attempting to flash in the bootloader.
Before flashing in via the ICSP port, make sure to TURN OFF ALL THE DIP SWITCHES FIRST!
Specifically DIP1, 7 & 8. Doing so will power down the Bluetooth module, reducing power demands on the 3.3v supply - helping to assure we have a nice stable source while flashing the bootloader. It will also free up SCK and MISO pins from being pulled hard to ground, preventing them from working and perhaps also causing damage to your ICSP device.
None of this is needed while loading sketches / firmware via the Serial adapter (Normal Arduino way). It is only critical when using the ISCP port.