Why not sterilise it with Armillatox.

What do you mean by unsterilised compost? Only I have never sterilised the compost which I get from my compost heap. The compost one buys in bags (ie potting compost) is only sterile until you open the bag and then very quickly picks up bacteria fungal spores etc. from the air very quickly.
We use both and I cannot say that the compost has ever caused any problems.
Now there has been trouble with manure contaminated by a hormonal weedkiller (will remember the name eventually). That has been a real killer for those caught by it.
The tomato problem could well have been Blight for example and the roots being attacked a secondary result of the plant dying.

Aminopyralid Owdboggy, It was certainly causing big problems last year...or rather the year before (keep forgetting we're in 2010) :-)