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I have wired up pins 0 - 13 and used the code you provided. I can see pin 2 – 13 blinking and pin 0 and pin 1 are tied high. Are these the same results you are getting?
Add to the file <arduino-1.5.3>\hardware\arduino\x86\cores\arduino\ wiring_digital.c after line 143 the following:
if ( pin == MUX_SEL_UART0_RXD && mode == OUTPUT)
if ( pin == MUX_SEL_UART0_TXD && mode == OUTPUT)
Restart Arduino IDE and that should fix pin 0 and 1 to be used as digital output.