My netbook has this problem, too. If you enable custom templates
creating any custom template) everything works again.
I noticed that the inbox for any account does not have the per-folder template
customization. This should be different on kde 4.3 as I don't remember it
Something else that I have noticed now and that is in line with the problems
The "automatically insert signature" feature was turned off in the preferences
although I have not touched it ever. So it seems that changing some options
leads to other being changed. :-(
Actually it was what happened to the default template, it changed to %blank
The same occurred to other options that have been changed on my back.