Just because this took a lot of research from me (Looking at specs), I am posting this here for my own reference.
Note: CF cards will work on both 3.3V and 5V. so there is a bit of a mystery on why we need a voltage step down chip and a jumper for this particular adapter, other drives are clearly incompatible IDE interfaces.
it turns out that when combined with a converter using the fc1307a chip to create CF out of 2 SD cards, it will not work without a voltage step down, with the wrong setting, or with cards with no step down, a computer will see the combined cards, but will fail when trying to format them for some reason.
The 1.8″ adapter (Sideways IDE interface) is 3.3V, the normal 2.5″ disks are 5 Volt, the adapter we have that turns CF cards into 1.8″ or 2.5″ compatible drive, has a JUMPER to select, this jumper effectivly activates or deactivates the voltage step down chip (The only chip on the board)
So there you have it, 1.8″ and 2.5″ PATA drives are not compatible regardless of the fact that the PIN interfaces are the same. the adapters with a voltage step down will work on both, but you need to set them up first with a JUMPER