I had the exact same problem after building my Win7 MCE box a couple of months ago...although without knowing what hardware you're using, it's impossible to say if it's the same cause.
My OS/apps drive is an 80G Raptor, so it resumed from S3 just fine, but the IDE storage drive was always MIA until a reboot.
My Bad Axe 2 only provides a single IDE port, and I assumed because of the drive orientation that I needed to make my Plextor 708A the Master, and make my Caviar 250 the Slave. After all, conventional wizdom was that the device at the end of the chain on Blue should always be Master. And I've historically had bad luck with CSEL, so I didn't even try that.
Took a shot in the dark: I swapped the jumpers to force the Caviar to be Master and the Plextor to be Slave, without reconfiguring the drive orientation. Worked like a charm: my Caviar always comes to life after S3 resume.