Found this message
This should never happen:
If you know how to reproduce this, please contact the program author.
And could reproduce. Here are the steps required, the files are in the attachment:
1-Compare Folder "1" with Folder "2"
2-Double click 1.txt
3-Click Merge Current File
4-Select Merge->Choose B Everywhere
5-On First Diff: Deselect B (Press Ctrl+2) and Select A (Press Ctrl+1)
7-Go To Next Diff (Ctrl + Down)
8-On Second Diff: Deselect B (Press Ctrl+2) and Select A (Press Ctrl+1)
9-Save (Ctrl+S) -> mergeResultSaved: m_pMFI=0