I have an "Open With" command to open both files in TextPad:
TextPad.exe "%f(%l)" "%f(%l)"
In build 3.0.2.8706, this still works for 2-way merge. However, for 3-way merge, it opens the first file "D:\Dir1\Dir2\File.txt" correctly, but attempts to open the containing folder "D:\Dir1\Dir2" for the second file. It appears to be launching the application as follows:
TextPad.exe "D:\Dir1\Dir2\File.txt(10)" "D:\Dir1\Dir2"
With an extra "%f(%l)" parameter, it attempts to open the containing folders for the second and third files.