for 4.2.4 or higher, 4.2.5,4.2.6,4.3.7, it's works, this is the way which makes Always in evaluation mode.

1. open Terminal, go to the dir : cd /Applications/Beyond Compare.app/Contents/MacOS
2. change the name BCompare to BCompare.bak: mv BCompare BCompare.bak
3. touch a file name BCompare , and chmod a+ux BCompare : touch BCompare && chmod a+ux BCompare
4. open BCompare with text editor, insert the script :

#!/bin/bash
rm "/Users/$(whoami)/Library/Application Support/Beyond Compare/registry.dat"
"`dirname "$0"`"/BCompare.bak $@