I now stumbled upon similar case, if not the same with another board. I was able to connect access point of Omega2S and open putty to run commands. After I have run command wifisetup and select option 1, link with omega broke, and I think it also rebooted. I'm not sure about all circumstances, as I didn't connect via serial port.
Then I made conection with O2S again and check ifconfig.
I noticed that there is suspecious eth0.1 interface. So I decided to run command ifconfig eth0.1 down to disable that interface.
Then I tried to run wifisetup and this time it was succesful! I managed to finish instalation of all needed software and it works like a charm.
I can't check if it's the same with one that I had problems with, as it is not on it's board anymore, but for this one it worked.