I'm removing the text of my answer because it's so inaccurate it's embarrassing. I mistook "B2B" for "Enterprise" and answered based off of that. To make up for it, I'll look into the problem a bit more and if I find anything I will edit this answer accordingly.
Edit:
Okay, I can see why you put a bounty for this question on SO; there's not really any data on a problem like this anywhere. Frankly, there's not much available information on B2B in general. I'll post what I found anyway, in case it can be of any help to you.
I found the details reason behind Maggie's question, there. Per Editing and Updating App Information:
Updates keep the same Apple ID and bundle ID, which means they are
associated with your first version and free to your customers
Also, apparently, "You can't change the CFBundleIdentifier of a released app if you want to release updates for it, the App Store will automatically reject it when you upload." which is something I can vouch for, having experienced this with a normal app. I do know that for a B2B app you do have to submit it to Apple for review, but I can't tell from the documentation I found if you need to actually submit it to the App Store, so it may not go through the various checks that normal apps go through, so this could be your problem.
Aside from that, according to the VPP guide, if your customers are installing the apps on the devices with Apple Configurator (broken right now, per app store reviews) the updates also have to be done with the Configurator. You haven't said that Configurator was involved, but I did find this tidbit.
• Use Apple Configurator to install apps on new or supervised devices.
Apple Configurator on a Mac makes it easy to mass configure and deploy
devices that are centrally controlled. Redemption code spreadsheets
acquired through the Volume Purchase Program can be imported by Apple
Configurator, tracking the number of apps installed on each device. To
update deployed apps using Apple Configurator, you must reconnect to
the same Mac from which the apps were installed. Learn more at
itunes.apple.com/us/app/apple-configurator
Anyway, good luck. Wish I could be more help.