Infinity IRS Betas Make Loud Noise When On

Not familiar with Betas but it's probably similar to the RS1Bs that I run. The servo unit is phase dependent, the phase has to be be correct. It sounds like the amp or pre-amp might be inverting the phase. You need to find that out and then connect accordingly. I have a couple of servo controllers but they are a pain to run. Your servo controller is going into protect mode. You are lucky the early models would just blow. They often have hum. One of my units worked fine and then started humming out of the blue so that is when I scraped it (saved it for the next guy).
I have run my system without the servo controller, just using a crossover and it works fine at the levels I normally use. Those systems are state of the art and finicky. Trouble shooting is difficult and not much fun.

When I hit the power button on the xover, I hear both. As soon as the green light comes on the xover, it pops really loud and it goes into protection mode.

If one of the AC outlets that your various components are plugged into is wired out of phase; you can experience the same result as the mis-wiring of the bass Management system and towers. An inexpensive tester such as this, can tell you if that's the case: (http://www.amazon.com/Sperry-Instruments-GFI6302-Outlet-Tester/dp/B000RUL2UU/ref=pd_sim_469_1?ie=UTF8&refRID=1GVME041151YJ24Q6J9T&dpID=51mLOd%252BDHqL&dpSrc=sims&preST=_AC_UL160_SR160%2C160_)

What goes into protection mode- the amplifier?

I am not sure that there is anything awry with your system. The servo-crossover should be turned on before the bass power amplifier(s). When first switched on, the red "power on" indicator should illuminate, and the green "servo on" should come on a few seconds later. It's then safe to turn on your amplifiers.

As the manual explains, if your preamp has two sets of outputs, you can wire the mid/hi frequency panels directly to your mid/hi power amp. That is the preferred way to connect this system.

When powering your system down, the best practice is to turn the amplifiers off first, and then the servo-crossover.

You should also check the gain of your bass amplifier(s) and set the open loop gain compensation switch (on the servo-controller back panel) accordingly. Note that especially if you are using bridged anplifiers, you'll need to reduce the gain with that switch.