Hello Alex.
The timeout issue still persists, but I've done some testing during the week which I'm hoping may help you to resolve the issue.
As a recap, I tried a different computer, I have tried powered internal and external USB hubs, USB2 & 3, and 3 controller PSUs, all to no avail. I have also tested it with a different controller. I had previously used PST Rotator without error, so I set that up as a Hamlib server and the problem still persists.
What I have noticed is after launching SatRoof, if I select a satellite to track, be it within the next 10 minutes of the next ten hours, the program patiently waits until the AOS event. However, shortly after the pass completes, SkyRoof throws the same error. If I click ignore and select the next pass I want to track, SkyRoof just waits until AOS, and then shortly after the pass completes, the error displays again.
I'm out of ideas Alex. Can you throw any light?