Thanks Stutho, I may try the PTFE tape idea if the problem re-occurs. I am using a square sectioned spindle in thorn cranks. It is possible that greasing these up may have been the solution. However, when I reversed the original chain and also when I fixed a new one the problem stopped for a few days before returning, which leads me to think it is something to do with the EBB. At the moment the chain is quite tight but different tensions didn't seem to affect the irritating click. I've now got a PC68 chain and I am using finish line green oil, the PC48 chain had only done 1600 miles and is now a spare.
When you remove your BB do you leave the eccentric in place on the bike? As I mentioned above this resulted in the EBB moving and some damage.