I use a windows laptop running Zwift, that is where I do my pairing and I use an ANT+ dongle. I also run the companion app on an iPhone. I never have any problems getting it up and running over the last week there have been a few issues with the companion app, none with my windows connection. I'm also using a wireless router.
I think that running the program and Zwift on the same machine is asking a lot of that machine. But I have to say, knock on wood, my set up has been very reliable for the last 11 months, i use Zwift on average 6 days a week. My words of wisdom to the OP is try different hook up methods, perhaps if you are using the companion app on the same device as the program try pairing in the program and not using the companion app.
Some users on BF complain that it takes too long to connect. I find that with all of the futzing I have to do getting ready to ride the program is ready before I'm ready.