[JFreak]

I fear there is something going on with the OMNI, so please try to isolate the problem by only connecting the three HD interfaces together and see if they work nice with each other.

If that is a success, then try it the other way around. First only connect the OMNI and verify that it is okay. Then connect one HD interface at a time, leaving the OMNI as first interface, and see if you can loop sync one, two or three HD interfaces to the OMNI. One by one.

If that is success, then just choose the clocking device from hardware setup. I think HD interfaces have better internal clock than the OMNI. And no, the clock master doesn't need to be the first interface. If the system works when OMNI is the first interface then just let it be so and choose the clock source you want.