I believe this may be related to duplex scanning, but I have a user running a Brother 8480DN scanner and when they scan through the Twain interface Every other page comes in upside down. I have tried re-installing the scanner software to no avail. I think the next step is to disable Duplex scanning and see if that helps. I am not sure if there is much else to try given that the scanner control settings are coded into our DI modules and the users really have no control over that from within our application. But I have not seen this with any other scanner model we use currently so I am trying to figure out if it is specific to this model.