The console window should continuously update with http requests from the desktop app.
Exit out of the tray app completely. Then open the task manager. Do you see pyTivo.exe still running? If so kill it. (there will be two copies, this is normal, kill them both) Also if you have the old pyTivo service running you need to stop that as well as it will cause a conflict. After that relaunch the tray app and start desktop, does it work now?
When I exited out of the tray app, there were still 2 copies of pyTivo.exe running in the Task Manager. I killed them and then repeated the test. This time, I did see continued http requests when I ran the desktop app.
Here's the output from the console window (which seems to keep repeating but I didn't copy all the repeats):
INFO

yTivo:192.168.1.110 [17/Apr/2017 16:56:56] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.1.113 [17/Apr/2017 16:56:56] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.1.112 [17/Apr/2017 16:56:56] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:20] "GET /TiVoConnect?Command=GetSettings&Container=Settings HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:20] "GET /TiVoConnect?Command=GetTiVoList&Container=ToGo HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:28] "GET /TiVoConnect?Command=GetQueueList&Container=ToGo&TiVo=192.168.1.110 HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:28] "GET / HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:38] "GET /TiVoConnect?Command=GetQueueList&Container=ToGo&TiVo=192.168.1.110 HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:38] "GET / HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:48] "GET /TiVoConnect?Command=GetQueueList&Container=ToGo&TiVo=192.168.1.110 HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:48] "GET / HTTP/1.1" 200 -
INFO

yTivo:192.168.1.110 [17/Apr/2017 16:57:55] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.1.113 [17/Apr/2017 16:57:55] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.1.112 [17/Apr/2017 16:57:55] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:58] "GET /TiVoConnect?Command=GetQueueList&Container=ToGo&TiVo=192.168.1.110 HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:57:58] "GET / HTTP/1.1" 200 -
INFO

yTivo:127.0.0.1 [17/Apr/2017 16:58:08] "GET /TiVoConnect?Command=GetQueueList&Container=ToGo&TiVo=192.168.1.110 HTTP/1.1" 200 -