1. Not all hard drives are created equal when it comes to seek times. On top of that, some hard drives have super aggressive power management and will park the read/write heads more often than others, resulting in even worse seek times and overall bandwidth.
2. Defragging a hard drive is a bit of a misnomer. The process in Windows defragments individual files so that all the bits of ONE particular file are physically stored in only one area, but it doesn't magically group multiple files together (i.e.: all Unigine files in one sector), so the head still has to access multiple locations on the disk to run programs and load game assets. To optimize your HDD beyond what Windows defrag does, you need another program.
3. BFG is correct that these scores are within an acceptable margin of error. Every new HDD you add, Windows will adjust its virtual memory pool (page file) for each drive. You could try disabling the page file on the D drive so Windows reverts to only using the C drive, like before. It's worth a look.
4. Some engines are more sensitive to HDD performance than others. Unreal Engine does this ALL the time. SSDs have all but eliminated the stutter this causes, but spinny disks really make it noticeable. Games that are 32-bit that use more than 2GB RAM most commonly will repeatedly hit the page file when loading environments or while streaming textures. If you have an option to run the 64-bit version of a game, do it (if you have enough RAM).