mneumayer:
I'm working in Linux Mint 13 and i'm using the software from the Arduino website.
It's possible that AVRDUDE is left running and has the port locked up. In Linux, try this:
lsof | grep -i "tty[ACM|USB]"
This will show you all of your ttyACMx and ttyUSBx ports that are in use.
If AVRDUDE is using one, kill it by process number or with this command:
killall avrdude
Then try accessing your board again.
Hope this helps.