I will say I found a key to starting up so many... it takes the USB's (at least the RHB-500) a few seconds to recognize that a computer (in this case the rPi) has been turning on, if I were to let MinePeon boot normally it would only see about 54 erupters (as the other usb hubs are still "turning on" (realizing a computer is there) you can tell this on the RHB-500's due to the nice green indicator light at the front of the hub. So, I delay the miner start up on boot by 20seconds... which corrects the issue and allows for the hubs to "start up" and always boots all 64 without issues if I ever have to reset.
How many BEs are you able to run on each of those RHB-500 hubs? Did you upgrade the PSU on them?
8x Erupters per hub, I didn't have much luck when trying to switch them to running off a PSU, I had a cheap 450watt and I hooked up one of the hubs to it, had problems running 6x Erupters... I may try tomorrow with a different PSU, but I'm fine running 8x per, it's been stable over a week this way.