Messages in Storage folders corrupt after importing – either duplicates, or ‘Message not Found’, or some are correct.

After reinstalling Windows 7 64 bit, & Windows Live Mail, I imported messages through the built-in export/import method.  There was a hierarchy of folders, but I moved them so there was just one level & deleted the empty unneeded folders.  All looked fine, until I checked the actual messages.  Messages in a small number of folders are correct.  All the other folders either have duplicated messages, or 'Message not Found' for each message.  I have the original import source if that would be helpful.