That sounds like a very frustrating shoot. The whole premise is flawed from the begining. First is the notion of trying to match the B camera to the A cam that way. There is an easier way to match two cameras. I had great success with this method on a feature I worked on last summer using two Cinealtas.
I brought the cameras together and matched them on the same white source taking care that the gamma curves were identical and black levels were matched perfectly. Then I saved the settings in the reference file on each camera. I also backed the settings up on a memory stick. On this shoot we only used preset white balance on both cameras and we corrected the lights if the white balance did not look right witch wasn't very often. For daylight we still used preset but corrected by changing to filter wheel D or A depending on the DP's wishes. If one camera woke up incorrectly I would simply recall it's reference file, Auto black balance and we were back in business. We only used a paintbox (RMB-150) on B cam when it was on a crane and needed to be rolled remotely. When I connected it to the camera I took great care to ensure that preset WB had been called and that the pedestal, gamma and knees were all in their detent settings. Another thing to remember is [/u]never hot patch the RMB-150. Connecting or disconnecting the paintbox while the camera is on will throw it into fits.
The "format error" that you got when trying to save to the memory stick I've seen when using MS's that have the "Magic Gate" on them. For whatever reason these MS's need to be formatted on a PC then you can use them in the F900. Ask Sony why.
This is my first post let my know if I was helpful. DetroitDIT (Don't panic... it's only ones and zeros)