Hard to say what went wrong without more information. Either the cloning went bad and you have incomplete rootfs clone on mmc (i.e. you forgot to use GNU tar) or you cloned already broken system. If you really cloned something that is working in flash and not working on MMC and your copy is complete than we have unknown problem :-) If you want to troubleshoot this see https://maemo.org/bugzilla/show_bug.cgi?id=838 for description how to verify if you copy is exact.

The easiest way to have this working is to reflash with clean system and clone it before you break it with additional unstable packages.