Mike are you in the UK ? There is a great company called supreme motorcycles [no connection] in Leicestershire who will sort it out, they are Ferodo brake specialists and can fit your shoes with very good quality linings.
it sounds to me like there is some sort of contamination on your linings which is gassed off when you warm them up, but returns upto the surface overnight.
I once had a car that would nearly throw you through the windscreen in the wet when the brakes were damp and cold, but was fine when they had been warmed, I had them relined and they were great. the garage said they had oil contamination on them, maybe this is a similar problem.
BTW, those charcoal grey linings you can buy are not the best at all. I assume they are bonded, and you have checked they are secure, they have been known to come loose at the ends.
Here's their website good luck.
http://suprememotorcycles.co.uk/