I am pretty sure both ends of a scsi chain need to be terminated, so that means you need to leave the terminator in place on the motherboard. The SCSI controller is the first end of the chain, and the very last drive in a linear chain from there will need termination.
In section 4-12 of the A3000 owner's manual, it says this:
"If both internal and external add-on SCSI devices are present, the termination resistor packs must be removed from the original hard disk for proper SCSI operation."
Also, make sure each device has its own unique SCSI ID, and keep in mind that the controller takes 7 and by default the first internal drive is set at ID 6.
There's more information in section 4-23 of the user manual.
EDIT: after re-reading the post, I believe you have a termination issue. There is an additional terminator somewhere that needs to be removed and then moved to the last physical device on each end of the chain. The last device on the external connector needs a terminator and the last device (think linearly -- the very last one on the ribbon cable) needs termination.
If you are using internals only, the terminator should stay on the motherboard OR you can take it off and place an external terminator on the external SCSI and a resistor pack terminator on the last internal device.