SB800 issue

"I  just got a Nikon SB-800 off eBay, and I was toying around trying to take some pictures with it, but noticed an issue...

My batteries are pretty weak, So i'm going to try a fresh set and see what happens i guess. 
I changed the flash mode to manual for the heck of it, and it fires after the shutter opens and contributes to the exposure. It only seems to fail to expose correctly in TTL mode. 
Am I doing something wrong? 
No matter what I change, Sync speed, minimum shutter speed, etc... the flash appears to fire BEFORE the shutter actually opens and doesn't contribute AT ALL to the exposure. 
I'm using it on the hot shoe of my D200, TTL mode, Aperture priority, 55mm focal length, aperture is 5.6. Flash sync speed is set to 1/250(auto FP) minimum flash shutter speed is 1/60.