I've contacted Altera about this matter and I thought I'd give an update.
Basicly they are all bugs.
That all the options become available when you import a Quartus 9 project into Quartus 10.0 is a bug they didn't know about yet. I quote:"
In v10SP1 the following transceiver options should be available (and no more): TX/RX Bandwidth, PPM threshold, ATXPLL, Receiver Analog Settings, Transmitter Analog Setting, Starting Channel Number."
They will try to fix this in the next release coming in December 2010.
They were a bit vague about loopback being a bug or not. What I am sure about is that at the moment it is not possible. Everything should be working right, but they they basicly didn't bring out the enable signal, so it's not available to choose atm.
Now I will have to loopback via a switch, which is ofcourse a lot harder to accomplish.
Also there is a rxgxbclk clock signal that is internal but brought to the outside in case people want to use it. This signal is not documented though as being an useable signal. But you can just leave it open if you don't need it.