CPU fan(Stock i5 fan)->CPU Opt on Mobo continues to run
200mm Case fan->fan controller->CPU fan on Mobo doesn't run
120mm Case fan->fan controller->CPU fan on Mobo doesn't run
120mm(Antec LED) Case fan->fan controller and Molex to PSU-> CPU fan on Mobo continues to run and use LED
As far as how long they continue to run, I haven't actually seen them stop spinning. The first day I noticed the problem, I woke up and the fans were spinning from when I thought I had shut the computer down the night before so roughly 7-8 hours.
Here's something else, I unplugged the Antec fan to see if it was causing some kind of residual power issue, and booted the PC up and shut it down again and now all the fans are spinning and it seems like they are spinning at a much higher RPM than what I have them configured for. Starting to think it could be the MOBO and not the PSU.