I did try this with Scotch Bonnets and they did go pretty yukky inside. Think it was something to do with air, but could have been any manner of things. Perhaps if someone knows why this happens (BBWCHATT?) you could avoid it.
I do as Chazza does but I freeze them on a plate, then scrape the frozen bits into a pot, that way it is 'free flow' when you need it. Do the same with ginger too.