It sounds like your drive is powering up in standby (PUIS). If so, then it needs to receive a read or write command before it will spin up. Otherwise, it can be configured to spin up in response to a particular Set Features subcommand.
See sections 4.19 and 7.48.8 of the following document:
Working Draft AT Attachment 8 - ATA/ATAPI Command Set (ATA8-ACS):
http://www.t13.org/Documents/UploadedDocuments/docs2008/D1699r6a-ATA8-ACS.pdf
WD drives have a PM2 jumper that governs this behaviour.
Jumper Settings Info Sheet:
http://www.wdc.com/en/library/eide/2579-001037.pdf
Otherwise, you disable PUIS via a software utility. I don’t know how to do this using WD’s tools, but Hitachi’s Feature Tool should work.
Hitachi Feature Tool:
http://www.hitachigst.com/hdd/support/download.htm
Hitachi Feature Tool Usage Instructions:
http://www.hitachigst.com/hdd/support/ftool_user_guide_198.pdf
