The other day I commented about being plagued with my external drives booting and running when I accessed items on my internal drive. As someone suggested Spotlight is the problem as it will index all external drives while one is running on the internal drive. To To prevent external drive indexing, go into System Prefs>Spotlight>Privacy. In this window you can choose anything including external drives so that Spotlight won't index them. Just select + and choose any drive (s) you don't want indexed.
MamaMoose
