terrier x 3 - I learnt something interesting in puppy school last week which might shed some light on the problems you're having. Dogs go through fear periods around the age of 8-16wks and 6-14months. Your puppy might become panic stricken about something they've seen/heard/experienced many times before.
The trainer said not to force the puppy to confront the thing he fears, but to be calm and non-fearful yourself. She said to treat the thing the puppy fears with disdain and he will take reassurance from you and not to over-protect or display too much concern.
Our 11 mth puppy went through a period of barking in the middle of the night for no reason - we would go out to find his hackles up and barking at nothing. This lasted for about 2 weeks and then suddenly stopped. If we had have known the fear period info at the time, we wouldn't have been so worried.
Hope this helps.