Have you had a time where you went to load an operating system onto your BlackBerry, and you start app loader only to see a message stating software for this device is not found? I have run into this issue a few times. The problem I have found is related to multiple registry keys for different builds that are installed on the computer.
These keys can be found at HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Research In Motion\Apploader\SearchPaths for 64 bit systems
HKEY_LOCAL_MACHINE\SOFTWARE\Research In Motion\Apploader\SearchPaths for 32 bit systems.
For whatever reason, when there are multiple builds it may default to one that is not for your device or to an undesired build. One tool that I have found useful is revo uninstaller there is a free version of the app which is really good.
When I work with hybrids I copy the whole folder then uninstall the build. I do this each time so that the only folder and registry key sitting on your computer is the build that is desired. When you do this, along with deleting vendor.xml files it will make sure your upgrading and downgrading processes are as smooth as possible.