Sure OS3.9 supports HDD's larger than 4GB. But are you u sure that you enabled "automount partition" in HDToolbox? Or are the jumpers set correct? Btw, i have maybe a similiar problem too.
I have a 30GB and 120GB HDD. The 30GB is my boot HDD where the SYS is installed. The 120GB is for storage and backups etc.
The problem is, when i keep them both in the same IDE line, the 30GB (smaller) HDD won't boot because the larger 120GB HDD get's the highest priority and prevents the system to booting. Even when i have the jumpers set correctly and "bootable" isn't checked in HDToolbox.
Try to put the 10GB HDD on the other IDE chain and try again...
