I didn't get anywhere attempting to pare down the problem.  So I went 
looking in the code.  In "callbacks.c" the routine 
"callbacks_change_layer_edit_clicked" does something highly suspect.

   transforms = g_new (gerbv_user_transformation_t *,
     mainProject->last_loaded +
     2 /* layer + NULL */ +
     1 /* if selected layer is visible */);

 From what I can tell, g_new will allocate an array of pointers to 
transformations, without actually allocating any memory for those 
transformations.  Furthermore those pointers are initialized nowhere. 
Code that looks something like the following might work better.

   transforms=(gerbv_user_transformation_t **)
     malloc(sizeof(gerbv_user_transformation_t *) *
     mainProject->last_loaded+3);
   if(!transforms)
     abort();
   transforms[0]=(gerbv_user_transformation_t *)
     malloc(sizeof(gerbv_user_transformation_t) *
     mainProject->last_loaded+3);
   if(!transforms[0])
     abort();
   for(i=1;i<mainProject->last_loaded+3;++)
     transforms[i]=transforms[0]+i;


On 2016-02-01 02:16, Linda Huxley wrote:
> Hi Sergey,
>
> OK, I'll see what I can do to simplify the problem.  I wanted to mention
> that I noticed that (for those particular Gerbers) the problem appears
> on the square pads on all "8" 3M MDR connectors on that board (4
> connectors are 20 pin and 4 are 50 pin).  It is highly likely that those
> are the only 8 pads with that "aperture" size.  So perhaps it is the
> aperture table that is being overwritten in that case.
>
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