Try closing the TCMD window yourself while the updater is downloading the new build and see if that makes any difference.
To install build 53, I ran "option /u" and then immediately exited from Take Command, leaving ShrAlias running. The Windows Task Manager showed one copy running.
When the setup program asked for permission to close ShrAlias, I selected OK. The ShrAlias task disappeared from the Task Manager.
When the successful install message came up, there were still no ShrAlias tasks running.
I clicked on the "Run Take Command x64 17.0" button. By the time the registration dialog box came up, there were now two ShrAlias tasks running.
After Take Command started running, I executed "shralias /u" twice. After the second time, I got the "SHRALIAS unloaded" message, but a command prompt never appeared. I started a new tab and killed the original one. I could then run ShrAlias to get it running again.