@Anthony-Kelly You might try unplugging the omega from the dock and putting a small piece of jumper wire between the receive and transmit connectors of the connector the omega sits in (just be careful to get those and not power lines - a 1k resistor would work too, and be more tolerant of mistakes).
With the wire in place whatever you type in a serial terminal should echo back, without it the echo should stop. That would test the USB-serial distinctly from the Omega 2.
Forgot about this topic for a bit. I did manage to get it working with the combination of the Omega1 tutorial and the new files from WereCatf. I had some problems compiling just the package, but I think that was my mistake.
About Lirc, I quickly abandoned it. It was much to complicated and bulky for what I needed. I ended up modifying some other code I found.
Thanks for your support. And @Chris Stratton you are right, capturing a thread is not so good. First I thought it could be the same problem. But you are right, without a serial console I cannot compare it. So i will buy a serial adapter and check what happens then. I will also check if I have a shorting.