Hello!
First of all, you can't run IDEFIX together with Elbox's IDE controller.
I'm running OS 3.9 with the Elbox IDE Controller, and it works great, but for some unknown reasons, the OS3.9 installation removes the ATA3.driver from the startup-sequence. You will need to add this line to your startup-sequnce again:
"dh0:c/ata3.driver" (if you have the ata3.driver file in your "c" directory, and if your harddrive is "dh0".)
This line must be in the top of the startup-sequence, before setpatch anyway. I have it as the first line in my startup-sequence.
If you don't want to see all your drives everytime you boot up your amiga, then you can add QUIET after the ata3.driver.
/Jörgen