Consider this Issue closed on my end. I have found that a combination of settings were conflicting with each other, and now am able to use both cards accordingly.
To those still having issues, might I suggest to check your V-Sync settings in your Driver software, and make sure it is disabled. As I have said, somehow, this is conflicting with the client and has cause me much grief.
Turning on triple buffering has somewhat reduced the amount of stutter, in single Gpu, but removing V-sync altogether is what brought my second GPU back online.
I hope this helps.