[Gmsh] Physical Points have wrong position in mesh

[Kaffeeheblerei]

Dear all,

I have modelled a structure which I want to compute with Calculix. For the
boundary conditions I set Physical Points. Unfortunately the exported mesh file
(.inp) referes to different points (other coordinates) for the given NSET. Is this a
known bug and is there a workaround?
Strangely it happens only to "some" of the physical points. Some have a correct
reference. 
I tried to make a small working example which I can post here, but it seems
like this error only happens for larger structures (I don´t want to post the
whole structure here).

Greetings
Stefan