This is just a long shot based on a recent similar experience. I have a Humax HD PVR (Freeview) - OK, I know that's not a freesat version but bear with me.
A pal of mine has the same PVR, except that he has a Samsung smart TV and mine is an LG model.
The notable difference is that I AM able to watch the BBC's 3D offerings in side-by-side format from over Christmas in proper 3D, whereas he gets what you're getting; i.e. the only option not 'greyed out' being 2D>3D conversion.
I had a long read of his .pdf file manual, and the only thing I could find that would stop the viewing of 3D formats from an external source, i.e. via the HDMI inputs was that maybe the picture quality has been set at source to less than maximum. That is to say, if you've accidentally got your Freesat box set to output at, say, 576i or 576p, you can't have 3D but once it's set at 1080p, the extra 'real 3D' options reappear.
(I'm not sure if my pal has sorted his outputs from his Humax box yet, as curiously it's a wholesale reinstall, involving losing timers and a needing a retune. I was amazed to find that nowhere in its everyday settings can you change the HDMI output resolution. Maybe that's to prevent someone locking themselves out by selecting a resolution higher than the TV can stand, thereby leaving themselves with a blank screen!)
I have an LG tv model number 47LW4500-ZB. This tv is supposedly 3D ready. However when I try to show the BBC 3D transmissions (via Freesat) the tv does not seem to recognise them as 3D. The side by side picture appears but the only option I have in the 3D menu on the TV is '2D-3D'. The 3D side-by-side option is not accessible. Can anyone help please?