How do you compare them - by manually selection or by passing parameters from third party tool? Normally Compare It! dislpay file names as it was given in parameters.
Using total commander (6.52)
I used %p%n %t instead of %P%N %T.
It is interesting
%p%n %t works but displays fle names with "~"
%P%N %T comes with "destination file not found"
%P%N %T%M seems working (but not all times)