John, I was facing this issue on 02/09/2018 and here is the log, what is the version of tool which has these bugs fixed, Today I see version 1.2018.821.0 and that does not have option to sign the application. Do we have any documentation around the bugs fixed in latest version.
Following is log details,
[9/2/2018 10:09:50 PM] [Debug] PackagingStart
[9/2/2018 10:09:56 PM] [Debug] PackagingStop
[9/2/2018 10:09:56 PM] [Debug] About to start process
[9/2/2018 10:09:56 PM] [Debug] - File name: signtool.exe
[9/2/2018 10:09:56 PM] [Debug] - Arguments: sign /a /v /fd SHA256 /f "C:\Users\Admin01\Desktop\Test.pfx" "C:\Users\Admin01\Desktop\TestMsixPackage.msix"
[9/2/2018 10:09:57 PM] [Error] signtool.exe failed, exit code = 1
[9/2/2018 10:09:57 PM] [Error] Error occured: Microsoft.Packaging.SDKUtils.ProcessRunner.ProcessRunnerException: Process signtool.exe failed with exit code 1.
at Microsoft.Packaging.SDKUtils.ProcessRunner.ProcessRunnerBase.ValidateExitCode()
at MsixGenerator.MsixPackageGenerator.RunSignTool(String packagePath, String certificatePath)
at MsixGenerator.MsixPackageGenerator.FinalizePackage(CancellationTokenSource cancellationTokenSource)
at MsixPackagingTool.ViewModel.Common.ViewModelBase.CreatePackage(Object sender, DoWorkEventArgs doWorkEventArgs)
at System.ComponentModel.BackgroundWorker.OnDoWork(DoWorkEventArgs e)
at System.ComponentModel.BackgroundWorker.WorkerThreadStart(Object argument)