I confirm the problem.
Have a SiI3114 SATARaid downgraded to a SATALink (i. e. flashed with a plain IDE BIOS) in an ECS P6VAP-A+ motherboard (VIA VT82C694X) -- and can't boot from any of the SATA drives attached to it.
The problem is indeed between the motherboard BIOS (Award 6.00PG) and the PCI card, as, once booted, even plain MS-DOS 6.22 sees the SATA drives.
As a workaround, I can suggest that you buy a simple SD2IDE or CF2IDE add-on card, attach it to the IDE controller and plug an SD card or a CompactFlash into it. The SD or the CompactFlash can hold as little as IO.SYS+MSDOS.SYS (Win9x) or BOOT.INI & friends (Windows NT), be rarely written to and last many years. At least, that's the path I'm about to take.
CompactFlash per se is electrically compatible with IDE (i. e. it has the same 40 pins), and, additionally, there're CF to SD adapters (so, being short of CF cards, you can plug an SD card into a CF2IDE expansion card). Below is what these cards look like. Both flavours have a Berg power connector:
Update: SiI3114 is fully bootable.
I managed to boot MS-DOS from SiI3114, using a 128-GB Intel SSD drive. The trick was to use fdisk.exe which came with MS-DOS to create an active 2GB FAT16 partition. Apparently, fdisk which comes with Linux, even in DOS compatibility mode and when using cylinders as the measurement units, is not 100% compatible when it comes to older OSes and creates misaligned partitions.
To DOS and DOS-based OSes (in terms of their boot process, like Windows 9x), SiI3114 appears as yet another IDE controller.
So, if you have an Award BIOS, be sure to select HDD-0 (as opposed to SCSI) as your boot device: