You might be running into the 1024 sector issue. Where in, anything after the 1024 sector on a hard drive probably won't be bootable. Also, Western Digital drives have been known to have issues with Linux. WD officially does not support Linux on their hard drives.
I would try this: Get a backup of whatever is on that 20 gig partition on the second HD, and then reconfigure the partition setup. Make a short (10mb or so) /boot partition at the beginning of that drive, then the 20gig windows partition, then the rest of your Linux partitions.