Finally got it working. I thought I'd post here about the mistakes I made.
First of all I knew the hardware was ok because not only did it work if I manually started sv_xbios.prg from c:\auto but we also tried with instreams sd card and it was fine.
But for some reason things wouldnt start from a clean boot, I tried with only driver in auto, driver before nvdi, driver after nvdi etc, nothing, no output on supervidel.
I tried a bunch of things and most of the time my tv complained about mode not supported followed by "searching for signal", I've not sure what that means but I figured it must have something todo with the resolution and/or colour depth.
Eventually I replaced what I think was a broken nvdi installation with a working one (5.01 instead of 5.11) because I would get the nvdi splash screen (init text) on the supervidel followed by sometimes an illegal instruction and most of the time once it had finished initialising its stuff I was back to what I had before, no output on supervidel.
Turns out I had also forgotten to replace SCREEN.SYS with SVSCREEN.SYS in assign.txt (I only got rid of the 'p'). Turns out that was a rather important step
and nvdi stopped crashing on me.
Next thing to try was to set a boot resolution, I replaced both modecodes in SV.INF with the same value which I got from setting the resolution manually using the dialog (remember I could still start the driver manually and get supervidel output), I also saved the resolution to NEWDESK.INF, not sure if that makes a difference but anyway..
Crossed my fingers and rebooted and voila! It started!
I think the main problem was that my tv didnt like the modecode in SV.INF, thats why things didnt work when run from auto, a broken nvdi installation just added to the confusion.
So thats it, thanks for all the help, hopefully this can help others in the same situation!