Let's start from scratch:
If you haven't done so already after updating your BIOS, please clear CMOS with main A/C power cable removed from PSU and load "Optimized Defaults" in BIOS after restarting the system (do not switch to AHCI Mode yet).
Tell us what kind of drives are connected to the system and make sure the drives in Question are connected to the Intel ICH9 SATA ports.
Now, there are a couple of locations were the BIOS can list the drives attached to your system:
1) POST Screen (Disable the BOOT LOGO in BIOS to see it properly
2) In BIOS: -> Standard CMOS Features
3) In BIOS: -> Integrated Peripherals -> On-Chip ATA Devices -> AHCI Devices Group
4) In BIOS: -> Advanced BIOS Features -> Boot Sequence
5) BIOS Boot Menu: Press F11 during POST to access it
Check each of these location for your drives when the system is in IDE mode and also when the system is in AHCI mode and tell us what you see.
but the BIOS doesn't see the drives when I switch from IDE mode.
The actual question is: Are you 100% sure that your drives appear in none of the locations listed above when you switch to AHCI mode?