Boot up problem w new hd

I just restored a system to a new hard drive because of a system crash. It was working fine until I put the old hard drive back in the computer for extra storage (it is ok). What happened was the system booted up from the new hard drive which it assigned as drive D but was running the programs from the old hd which was given drive letter C. I took the old hard drive back out again but now the start up on the new drive hangs at the light blue screen with the widows log and dark blue bands at the top and bottom right before you are ask to enter your password. I can restore again but I am hoping I can avoid it. Any suggestions?