|Was the swappable drive in it's bay when you did the repair?|
Did you remember to select which drive to Boot from in BIOS setup? You had to select Boot from CD to do the repair.
How is the swappable Bay connected to the Motherboard? Are your HDDs IDE or SATA? Both?
Double check all HDD connections, both ends. Just recheck all connections,PSU,Drives. Look for bent pins in Swappable Drive.
Your System Identification would be vey helpful, no Crystal Ball here.
On 2nd reading, it sounds like it's trying to boot from the Swappable drive. Risky unplugging the Swap Drive HOT.
There is nothing to learn from someone who already agrees with you.