This problem creeps up every now and then on certain rigs.
About what brent said, ICH10R should be set to 'AHCI' since you'll be attaching only HDDs to it and it does not support PATA.
Your PATA optical drive will be attached to a third-party chipset and that should bet set to 'IDE' in the BIOS.
Clean install OS as per usual. The first driver I'd install is Intel Chipset followed by latest driver for all the third-party chipsets such as LAN, Firewire and addon PATA. Lastly install the gfx driver.
To finish things off download Autopatcher and plug the holes up.
HTPC: E7300 | XFX GF9300 mATX | 2x2GB G.SKILL DDR2-1000 | Samsung F1 1TB | Slim BD-Combo ODD | HVR2200 & AverMedia TwinStar [4xDVB-T] | Windows7 x64 Ultimate
Server#1: Athlon II X4 630 | MSI 790FX-GD70 | Matrox 2D PCI | Samsung DDR3-1333 2x4GB ECC | Savvio 10K.2 146GB + DELL SAS 5/iR | 500GB 7200.11 | Dell PERC 5/E (+TBBU) | VMware ESXi 4.1
Server#2: Phenom II X4 945 | MSI 890FXA-GD70 | Matrox 2D PCI | Samsung DDR3-1333 2x4GB ECC | Savvio 10K.2 146GB + DELL SAS 5/iR | 500GB 7200.11 | Dell PERC 6/i + 8x1TB (+BBU) | Intel Pro/1000 PT Dual NIC | VMware ESXi 4.1
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