By default when setting Beyond Compare as the merge tool BCompare.exe is executed.  BComp.exe is the proper exe to use on windows for merging.  BCompare doesn't work for merging if a beyond compare window is already open since it will use that window and then exit immediately.

See: https://www.scootersoftware.com/v4help/index.html?command_line_reference.html

"BCompare.exe - This is the main application. Only one copy will run at a time, regardless of how many windows you have open. If you launch a second copy it will tell the existing copy to start a comparison and exit immediately.

BComp.exe - This is a Win32 GUI program. If launched from a version control system, it should work just fine. If launched from a console window, the console (or batch file) will not wait for it."