Experienced the same thing
I have 4 externals, one from lacie that always stays on, one from OWC that always stays on, but then a western digital mybook that spins up and down and a seagate that does the same. Post Leopard, the seagate and western digital would only spin up if I was accessing them or if I went to a save file dialogue. Now they spin up and down constantly, throughout the night, and for no reason I can clearly see. Quite annoying, as the western digi is very loud. Also, from what I understand, it is better for any hard drive to just stay in the "on" position and keep the platter spinning, as it is the spinning up and down over and over that could cause it to fail prematurely. For the record, I have not yet used time machine. I hope Apple fixes this, for it is certainly a bug.