A slow down could be from a couple of things. It could be that your boot sequence has the IDE drive ahead of your SATA boot drive (you can adjust this in your BIOS). Also, in your BIOS, make sure your IDE drive has 32-bit transfer enabled.
In Windows, your antivirus could be scanning the new drive and Windows index function could be indexing files as well. Accessing the IDE drive will be slower than when accessing the SATA drive as previously mentioned, but for data only that should be fairly insignificant.
Did you install any applications on the IDE HDD after you installed it?