Steve - running only one app and having recently reformatted the HD, in addition to having access to a fair amount of space does sort of knock out the "page out" suggestion. Well, I'm fresh out of ideas!
However, looking at the posts above, I'd say you're in expert hands now
... when Brad or Defiant or Kickaha or LoCash comes along, I usually just sit back and watch and try to pick up/understand as much as I can.
AI.org Tech Support - picking up steam ... I love it!
PS - once my power cable was faulty and this caused intermittent clicking on the HD (or it could have been the internal power supply)... is there anything there to check out?