For the loader you can use a java clone of the IFI loader I created last year.
http://shtylman.com/jifi/
Get the latest version (should be at the bottom of the list) for whatever platform you need.
I have verified it to work with uploading the new 3.0+ compiler compiled code on this years controller
For the serial port issue you have to remove a certain program. What is happening (and this happens for all USB-Serial converters in ubuntu default) is that a program called brltty (braille tty terminal) takes control of the device and then disconnects it. What is why you can't use it. To fix the problem just
sudo apt-get remove brltty and then plug the usb-serial converter back in and you should be set.