First one happens on a clear project without any localization settings ever made. Gather Text commandlet log has theese lines in it:
[2015.06.16-13.21.56:396][ 0]LogInit:Display: SourceControl:Error: Error fatal: pathspec 'D:/work/Unreal Projects/Myproject/Content/Localization/Game/Game.manifest' did not match any files
[2015.06.16-13.21.56:397][ 0]LogInit:Display: LogGatherTextCommandletBase:Error: Check out of file ../../../../../../Unreal Projects/Myproject/Content/Localization/Game/Game.manifest failed: Failed to add file '../../../../../../Unreal Projects/Myproject/Content/Localization/Game/Game.manifest' to source control.
[2015.06.16-13.21.56:397][ 0]LogInit:Display: LogGenerateManifestCommandlet:Error: Failed to write manifest to ../../../../../../Unreal Projects/Myproject/Content/Localization/Game/Game.manifest.
Bug is probably located inside a UGatherTextCommandletBase::WriteJSONToTextFile function. It first tries to add a manifest file to source control, but there is no actual file yet created, and it fails trying to add nonexistent file. Function returns and not actually writes content to a manifest file. If I disconnect from source control operation completes successfully. I am using git as my source control solution, other options may give different results.
Second issue arises when I have already created localization related files when not connected to source control, so they are not marked to add. Gather Text commandlet log has theese lines in it:
Head over to the existingAnswerHub thread and let us know what's up.