Problem with my Nikon R1 system not always flashing?

I just bought my 2nd Nikon R1 close up light kit… My first one would trigger both flashes no matter where I placed them (within proper distance). ( doing food photography, I was shooting a lot) But my new kit will not trigger both lights All the time… And it's not just one that doesn't trigger, it varies. I thought they wouldn't trigger if piled them on each other, that wasn't the case, I thought it was because they were pointing IN to the lens, that wasn't the case. It is TOTALLY random… The "troubleshooting" in the owners manual didn't fix any issues, and the batteries are bran new (well there's no date on the package).

I'm using a Nikon D90 with a Nikon SB900 head unit. The SB900 is set to 1 and A and the flashes are set to 1 and A. The SB 900 has the master and the slaves all set as TTL, and I believe the camera is set to the same. My last set did not require me to set the camera to "commander" mode because I always used the SB900 speed light as the commander/master.

Has anyone had this problem? And if so how did you fix it? I can always return the set for another one, but I have an important photo session coming up on Monday.

Thank you!

Added (1). I wrote SB900 "head unit" and I meant to type "Speedlight"

Added (2). So far I've tried "rebooting" everything while shooting, changing batteries, and moving around the flashes to be "in sight" and they seem to work a little bit more now, but still do not flash All the time. I'm going to give it a few more days of tests and then see where I'm then.

Any CLS issues I've had were always fixed by switching the camere off and on and by resetting the flashes.