What bios version is in the MPU? If you have the older BIOS it will not run H13.xx games. You may need a new bios. Also the Bally logo on the CF cards could be an issue. They have different drive geometry than a WMS card. I know the 64,128 and 256 bally cards work on a WMS, but I'm pretty sure the 512's are a different size and wouldn't pass validation.
As far as the top monitor. You are correct, may display gets DVI top display gets the VGA. You do not need to connect the TseTse for bb2 games. You probaly have to switch inputs to vga for the top box lcd in order for it to recognize the signal. For some reason the monitor automatically switches to DVI if it finds a signal, but it won't switch back to vga when there's none. The top monitor probably says "no input" or something similar?