This is actually a first time issue only.
This was always a problem with bleeding edge. When you updated your store to bleeding edge, we never actually saved information about the exact git commit that 'bleeding edge' referred to.
Without that information, core updater couldn't really check what files were modified. It always used files from latest stable version (1.2.0), and compared files on your server agains them. Obviously, any and all modifications to core files performed between 1.2.0 and git commit that was used for bleeding edge would be marked as 'modified by user'. Which is not correct.
From now on, core updater will store the exact revision inside _TB_REVISION_ constant. _TB_REVISION_ can contain either specific tag (1.2.0), or exact git hash like a09146c3db421e1604dd45dc8d63925c4aee7c4f. Core updater can use this information to compare your files with proper git commit.