External drive not letting go

I tend to turn on my external hard drive to backup my data at the end of my work day using Silverkeeper. When the backup is done, I try to eject the two partitions I've created on the drive so that I can turn it off.
Regularly, however, the system claims that one of the two partitions is busy and can't be ejected. This is after all backing up activities are complete and no applications are running.
Often, the external drive will indicate that it's being read constantly even though, once again, nothing's running on the machine. I've had to do a power off as I've lost control of the machine (the swirling ball is spinning) when I attempt to eject one of the partitions.
Any ideas what might be going on?
TIA,
David
PowerPC iMac, Dual Core iMac 20" (2Gb RAM), iPod 30Gb Mac OS X (10.4.9) OS X 10.3.9 on PowerPC

What you might be seeing is spotlight trying to index your external drive. Depends on what file system are you using on the partitions, spotlight might be unable to write the index file and keep indexing it every time you connect the drives.
To stop spotlight from indexing them, first try adding the partitions to spotlight's exclusion list in System Preference. If this doesn't work, use terminal to create an empty file by typing:
touch .metadataneverindex
place this at the root of the partitions will stop any indexing, but you won't be able to search that partition at all. Note that the file is invisible so you may want to turn on show invisible files while moving and copying it.

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