Although this is a year old post (original) the problem has been around for awhile. I have two Seagate FreeAgent disk drives powered by an externally powered USB hub, connected to my core 2 duo imac. The older drive 1TB, (two yrs old) is fine, never ejects itself, the new one that I bought last month, 1.5TB, is the culprit. Aside from making clicking, clunking and arcing noises, it will eject and reconnect itself several time an hour. I just downloaded the FreeAgent go sleep dmg referenced above,and installed it a few minutes ago, I will keep an eye on things to see if the problem has been resolved. I contacted Seagate a few days ago and and asked for a replacement since the new drive is only a month old, they sent an email today saying that they are out of stock. Both of these drives were originally formatted for Windows at the time of purchase, and i reformatted and partitioned them as GUID for use with OS X 10.6.
From the numerous comments about the same problem, independent of the brand of drive, it does appear that there is some sort of firmware glitch that exists between the Mac OS and the external hard drives. Now that Apple is aware of the ongoing issue, perhaps they will address it in the new OS 10.7, Lion??? Then again, maybe not.