Hi,

The following single command using the conditional operator in the 
Script window does the job: 

  Mbook3=mbook1>mbook2?mbook1:mbook2;

To count how many cells in MBook3 are equal to the cells in MBook1 
(assuming no same values common both in MBook1 and MBook2),
you can do the following (with a second intermediate matrix, Mbook4): 

  mbook4=(mbook3-mbook1)>0?0:1; //round up
  m2w method:=xyz;  //convert to a woksheet
  sum(col(C)); //get simple stats
  sum.N=;  //number of cells
  sum.total=;  //cells of 1
  sum.total/sum.N=;  //percent value

Hope this works for your task.

--Hideo Fujii
OriginLab