I gather this can be very confusing - I haven't really studied it as I don't have problems, but:
Read
Disk drive numbers may not correspond as expected to the SATA channel numbers when you install Windows on a computer that has multiple SATA or RAID disks
and
SATA port numbers vs assignemnt of Disk numbers/ - Windows 7 Help Forums
"At the device level, SATA and PATA devices remain completely incompatible - they cannot be interconnected. At the application level, SATA devices can be specified to look and act like PATA devices. Many motherboards offer a "legacy mode" option, which makes SATA drives appear to the OS like PATA drives on a standard controller. This eases OS installation by not requiring a specific driver to be loaded during setup but sacrifices support for some features of SATA and, in general, disables some of the boards' PATA or SATA ports, since the standard PATA controller interface supports only 4 drives. (Often, which ports are disabled is configurable.)"
"Advanced Host Controller Interface (AHCI) is an open host controller interface published and used by Intel, which has become a de facto standard. It allows the use of advanced features of SATA such as hotplug and native command queuing (NCQ). If AHCI is not enabled by the motherboard and chipset, SATA controllers typically operate in "IDE emulation" mode, which does not allow access to device features not supported by the ATA/IDE standard."
If AHCI is disabled you may get peculiar disk numbering and a confusing boot order.
Mac