Meld for merge does not mark conflicts as resolved since v2.0.0

What steps will reproduce the problem?

1. Set the latest stable Meld version as external program for merge: "C:\Program Files (x86)\Meld\Meld.exe --auto-merge %theirs %base %mine --output %merged"
2. Use TortoiseGit version 2.0.0 or 2.1.0

What is the expected output? What do you see instead? Meld opens with the correctly displayed panes and files, but after merging the correct values, saving and closing it, the file in TortoiseGit is not marked as resolved but is still "Conflict"

What version of TortoiseGit and Git are you using? On what operating system? TortoiseGit is 2.1.0 Git is 2.8.0 Windoes 7, 64bit Meld is 3.14.2 and has not been altered

Please provide any additional information below. Using the same Meld version and the same configuration for executing meld with the above parameters, TortoiseGit 1.8.16 used to mark the files as resolved, just fine.