I'm curious about the comment on this line:
DDRB |= (1 << PB1); //Set Pin9/13/PB1/ICP1 as output for PWM
Which pin on the board are you measuring?
HanFre:
Is there a difference in fuse bits?
The only difference is related to the different bootloader sizes:
uno.bootloader.low_fuses=0xFF
uno.bootloader.high_fuses=0xDE
uno.bootloader.extended_fuses=0xFD
vs
mini.bootloader.low_fuses=0xff
...
mini.menu.cpu.atmega328.bootloader.high_fuses=0xd8
mini.menu.cpu.atmega328.bootloader.extended_fuses=0xFD
of course that assumes the fuses on both boards are actually set to the Arduino defaults.