Many thanks to the Innotek-Crew who released VBox 1.6.2 today!
Now AMD-V is perfectly supported on my Athlon64-X2 and all my OS/2 installations now boot up without any problems and run stable! Host is Ubuntu-Hardy amd64.
(beforehand I needed a couple of boot attempts to bring OS/2 up and had to disable the global option 'catch keyboard on start')
I am running here original MCP2 as well as updated Warp4 flavours with drivers and kernel 14.104_UNI beeing by far more up-to-date than eCS 1.2r.