The solution was to turn off eArc on the TV and use Arc. And set eArc/Arc to auto on the Vertex2.
Also had to set the Audio Flag on the Vertex2 to 5.1. Seems there is a "bug" or interoperability issue when connecting the HD621 to the Vertex2 Audio Out, it can't read the EDID from the HD621 and you have to force it to 5.1.

Main: Marantz Cinema 50, Meridian 271, DSP7200.2, DSP5200HC, DSP5000 rears, Meridian 210.
PC/Headphones: Mytek Liberty II, Sansui CA-F1, Sansui B-2301, Sennheiser HD800, Kef R3