I was just about to give up on the FBV until I read the following info from the manual which seems to store programming in the device.  Would someone from Line 6 please confirm whether or not the FBV stores custom programmed midi commands when disconnected from the computer and if it will work with an iPad this way?

Opening and Saving FBV Presets

The Line 6 FBV Control application allows you to create, edit and save all the current settings within the application GUI as a “patch”, or FBV preset file stored on your computer hard drive. This means you can backup the complete settings currently loaded in your FBV Shortboard or Express MkII hardware’s internal memory, or numerous customized versions of those settings, as individual FBV presets and load any one of them into your FBV’s memory at any time. To follow are some details on how to manage FBV presets.

As mentioned earlier, whenever your FBV MkII device is USB-connected to your computer, and the Line 6 FBV Control application is launched with the device selected, the contents of the FBV device’s internal memory is automatically loaded into the Control application’s GUI. Additionally, whenever you edit any single setting in the Control application, the changes are automatically written to the internal memory of the FBV MkII device’s internal memory.

TIP: Even though all the settings within the Line 6 FBV Control application GUI are automatically stored on your connected FBV device, it is a good idea to always do a “Save” or “Save As” your current FBV device’s settings as an FBV preset on your computer once you have completed editing the settings. This ensures you always have a “backup” of all your customized settings that you can easily load again later!