One last set of questions, since I'm thinking of it...
1. Are you on an Intel chipset or an AMD one?
2. What drivers are you using (the vendor's or the default Microsoft ones)?
I ask this latter question because if the answer to #1 happens to be AMD, the various AMD chipsets are known to have SERIOUS SATA problems. Most people recommend running them in IDE mode if possible (annoying) though you can get decent performance out of them in AHCI mode as long as you DO NOT install AMD's drivers for them and just use the default Microsoft drivers. The AMD drivers with the SB750 and earlier southbridges are KNOWN to be horribly buggy. The absolute latest version of the AMD southbridge has, apparently, finally fixed much of this, but that only applies to AMD SB850 chips and later (which would be included in only an AMD 890GX or 890FX chipset board).
Unfortunately, it can be challenging to get Windows to revert back to the Microsoft drivers without wiping and re-installing from scratch. You usually have to uninstall the driver package from the Control Panel Uninstall Programs utility, reboot, and THEN go into Device Manager and delete the drivers there, making SURE to check the "remove software" box. Then reboot again and it SHOULD grab the Microsoft ones.
Likewise, it could be worth it to try updating the Intel Storage Matrix drivers (or whatever they call it nowadays). I've had random weirdness with some versions of those drivers, but the current version is working well on my systems currently.
Of course, all of this is moot if the problem does happen to be with MC directly, and it happens to me too. However, since you found one configuration with dual SATA drives that DOES work, in RAID mode (which is generally just AHCI with RAID enabled anyway), that lends me to suspect that you're seeing something more specific to that system. The system I'll be testing with will be an Intel P35 board in AHCI (not RAID) mode, so it should be a pretty good test.