I have a similar problem to this thread, but couldn't res. it: https://boinc.berkeley.edu/dev/forum_thread.php?id=13423

I am running BOINC v.7.16.11 (x64), wxWidgets v.3.0.1 on a Win10 box (fully updated).
I have been running Einstein & Rosetta for years, and have been having an issue with resource allocation since upgrading to a multi-core processor a couple of years ago.
I can't so much as run a browser window or run media without incurring skipping, despite having set priorities to favor foreground processes.

When I attempt to wiggle my mouse and wake up the computer, many times it does nothing. Ctrl+Alt+Del doesn't work. I can't see anything to try and end processes. Usually I do a hard reboot. Lately, I notice that Windows Update screens come up automatically, stating "Please wait while we get Windows ready. Do not shut down your computer."
This week, I did this 20 mins before my class (I teach) started. It was a full 35 mins before the update was completed. I was late, though I joined on mobile, so there wasn't a huge issue; I just lost a lot of functionality.
I have the settings set such that WinUpdate works at 2-3am. I suspect that BOINC projects are hoarding resources, and not relinquishing them to other higher-priority processes, including WinUpdate.

Apart from me creating a Python script to set BOINC Activity to Suspend whenever WinUpdate is triggered, is there something I can do?

In the past, I have found the best way to avoid my computer getting sluggish is to set the percentage of cpus in use to n-1 where n is the number I have. It hasn't been a problem on my new machine where I run a maximum of eight out of sixteen cores because of cache restrictions affect the type of tasks I run.

In addition to Dave's comments, it's good practice to lower CPU load if you are running GPU work to make sure GPU apps also have a full thread available. I like to keep one available for OS overhead as well. Using 8 threads / one GPU as an example, set Percentage of CPUS to 75%.

You can add an exclusive app in BOINC and it should suspend work while that app is running. In the manager, go to Options -> Exclusive Applications. You can also set a time schedule to allow for Windows updating or other tasks like backups, that's under Options -> Computing Preferences.

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It happened again last night, after leaving it on for a few hours, but this time, there was no WinUpdate. I had set the Max Cores as 75%, prior to it.
I have now set Max Usage as 75%, as well. This may be more like the other incident than I had previously thought, if it is just an issue with GPU.

Apart from me creating a Python script to set BOINC Activity to Suspend whenever WinUpdate is triggered, is there something I can do?

You could check how much memory your current BOINC projects use.
Especially with multi-core host and especially with Einstein@home project.
I found their current GW search impossible to support with quad CPU and 8GB RAM, time to time OS will crash due to low memory.
BOINC has an option to limit RAM in use so try to use it (Windows update tends to eat lot of memory too while running).

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Went to 75% of cores at max. 75% capacity each.
Taking away most of the input lag issues, but still turning black occasionally. Probably has more to do with the GPU than WinUpdate.