The query I made about the stem of my onions going brown before they were any any were near to harvest I think I have solved after much reasearch I have found out it is disease called onion 'smut'and it seems the best treatment is to dust the young plants with flowers of sulphur when planting out and dust again when they start to grow away.
This treatment is not guarenteed to stop the disease but it does give a degree of protection.