I finally got around to dusting off my playstation and I found I had a horrible problem with my controllers. The controllers would blink and not connect. The controllers would blink for about an hour before turning off. I tried googling this and could not come up a solution, it seems some people have even exchanged controllers to fix this issue.
Stumped, I decided to plug the controllers into the PS3 via mini-USB and this fixed the problem immediately! After discovering this everything fell into place. I often charge my controllers from my computer, since it is much more convenient, and it seems if you plug the controller into a computer with bluetooth capability (such as a Macbook) that the controller will bond with your computer and forget the PS3.
Solution: plug the controller into the PS3 via mini-USB