Hi Florence,
you should shift your local coordinate system to the global one. Then this problem should no longer occure. (Tanslationof your Head-BCs into the local system would also work, but this makes a model a little bit obscure).
This shifting is not very straight forward (I like to call it a graphical voodoo procedure...). You can find an explanation video on the FEFLOW support site (http://www.wasy.de/deutsch/produkte/feflow/support.html), look at the "How to's" on the bottom of the page and have some fun with it.
I asked the devellopers several times to get rid of this nasty thing. I would appreciate it if also some other people ask the FEFLOW crew for some change in this point. Maybe this would help. I can see no reason in this, and it is an error source, especially if the difference is not so big as in your case you may accept some wrong results.
Hope this will save your problems,
Zebra