Ok so if its recognizing both on the same cable, check the jumpers if your plugging one of the drives into a "master" plug with "slave" jumpers. If you have master/slave set specifically then try switching to "auto select" to give that a shot.
If you plug int a single channel you see both drives but doesnt load windows, So i would assume that you can put them both on the same channel, then get into your systems BIOS and modify the primary hard drive as it may be trying to boot the WD drive at that time.
Here's a review of how to set jumpers on IDE drives.
1. Always use the diagram on the drive to guide you. Do NOT use the diagram on one drive to set the jumpers on another. If your drive has no diagram, go to the maker's website and look up specs for the specific model you have.
2. A PATA data ribbon cable should have 80 wires in it. Start counting across it. If you get to 20 and are only ¼ of the way across, you're OK.
3. A PATA data cable has 3 connectors on it. The BLUE one on one end goes to a mobo IDE or PATA port connector. The BLACK one on the other end goes to the HDD you set as Master. The GRAY one in the middle goes to the HDD you set as Slave.
4. ONE HDD MUST be set to be Master using the jumper on the back edge and the diagram. Into this one plug the Black END connector of the data ribbon plus a power supply 4-pin Molex. On older computers, sometimes the Master drive on the Primary IDE port was the boot drive, but for some time now most mobo BIOS's let you set which device is the boot drive in the Setup screens.
5. IF you connect a second HDD on a data ribbon, it MUST have its jumper set to Slave, and into it you plug the Gray middle connector. And of course, it needs power.
NOTE that all this means that, if you move a Slave drive to a different IDE port and data cable so that it is the ONLY drive on that cable, then you MUST change its jumper to be the Master of that port, and you really should plug it into the Black END connector of that second cable.
The exceptions to all this is: You CAN set BOTH drive's jumpers to CS ("Cable Select"). Then whichever drive is on the END connector WILL be the port Master, and the one on the middle connector will be the port Slave.
My thought is are you sure it was the motherboard? If you bought a new board and still having drive/loading issues, it might be those "few bad sectors". I'd see about getting a new drive ASAP and start backing up data.