Probably the same issue I'm having here:
Running the command against a dir of config files apparently has issues because it does not always import in the correct order.
Additionally support has said that this can also be caused by duplicates config elements even though it should be a replace/merge type operation.
For some reason it seems like HP makes you look at several different docs plus online help to get all info about any particular things so I don't recall where I was reading it but it sounds like sometime you have to find out what piece of config is erroring and delete it eityher from source system before export of target system before import. Things like identical user names or ordering numbers can lead to this problem.
So much for an easy way to keep a test and prod system in sync!