Thanks.
Also does it when not connected to computer and in stad alone mode also.
It seems apparent now as from Motu technical support that it is a calibration issue on the spdif port chip within the unit.
Theres a procedure for connecting it to another unit(via spdif's) then opening up the case and turning adjuster screw until the noise stops.
Not ideal, but will do it when I get some time and hope it cures it (Motu says it will).