You are right... The code of MEMS_SetNeutral is the following: 
void MEMS_SetNeutral( void )
   {
   // Set Neutral position.
   MEMS_GetPosition( &XInit, &YInit );
   }
with:
void MEMS_GetPosition( s16* pX, s16* pY )
   {
   *pX = MEMS_Info.OutX - XInit;
   *pY = MEMS_Info.OutY - YInit;
   }
I guess it should be (to be tested): 
void MEMS_SetNeutral( void )
   {
   XInit = MEMS_Info.OutX ;
   YInit = MEMS_Info.OutY;
   }