Strange things can happen when you boot two hard drives that have OS on them and the drives are set active.
Do you have the jumpers set properly. I would assume you would want the new drive jumpered as a master and the old one set as a slave or cable select. Do you have the drives plugged in to the proper position on the data cable? (Master on end, slave on center)
It is possible that the Partition Table has suffered and will need editing. Go here
and download the free Partition Table Editor from Powerquest. It's a zip file but contains only one file so just open it on your Desktop. Run the executable and take note of how both of your drive partitions are labeled and post it back here. All I need to know is what type, such as type 4, type 7, type 12, etc.
Do not change anything in there just yet.