Nikon Flex tt5 and mini tt1 problem?

I'm shooting with a d700 with mini tt1 on camera hot shoe, with sb900 on top. Then using the flex tt5 with sb600 off camera. My problem is I can fire the sb600 off camera when I'm only using the mini tt1 on the camera hot shoe. When i place my sb900 on top of it for some fill flash the off camera flash stops firing or fires erratically (once in a while not every time. I have tried setting the sb900 as on, master, and commander and none of these settings change anything. I have done this setup before without a problem but I can't seem to do it again and am not sure if I'm forgetting a step or a setting? I really like to use the combination of off camera flash with on camera fill. Any one know what i'm doing wrong?

Added (1). @fhotoace I use the pocketwizzards because they can be fired remotely behind objects, they don't require the ability to see each other. I'm not looking for an alternative to using them just an answer on how to use them correctly

You do not need to use either Pocket Wizards

Just use the cameras CLS system through the SD900 to control the SB600 remotely.

I use my pocket wizards only when using studio flash and when doing so, turn off the TTL function of the TT5.