This will not fix the issue for everyone but I too had troubles getting the FBV Express MKII to be recognized by Monkey. I purchased the Spider IV 75 and FBV Express MKII just to find out I was unable to upgrade either one. The ratings on both devices were high so you can imagine I was quite disappointed to find out I had spent all this money and could not utilize the two to their full capacity. After searching around various forums and troubleshooting on my own, I was able to get Monkey to update the amp and pedal along with running the amp and pedal editor.
I'm using a Lenovo ThinkPad with Windows 7 64-bit. The laptop downloaded the driver without issue once the pedal was plugged in. I turned off the Windows firewall off and my AV as per suggested but that didn't work. I'd still do this step since it seemed to work for others. I also tried different USB ports and again that did not change for me but I would recommend others attempt this as well. Without the last two steps this might not have worked but what eventually worked for me was to run Monkey and choose any of the devices from the drop down (obviously not FBV Express MKII since that's why this forum was created). Once on the device page, I would plug in the pedal and choose Connect To Device. It would then recognize the pedal and allow me to perform the updates. I would do this same thing when trying to upgrade the Spider IV 75 which worked as well.
Upgrading was a bit painful as well. I had to disconnect the pedal and restart Monkey a few times and maybe even reboot the laptop but eventually I was able to get the amp and pedal upgraded. I also had issues when trying to have the amp and pedal editors recognize the device but I eventually got that to work.