I've had several problems with the BOINC manager and finally decided just to uninstall it. Doing so raises new problems for me.

OS: Ubuntu 16.04 LTS
BOINC: 7.6.31 (x64) obtained from Ubuntu Software store
Project: SETI@Home

Problem 1: After setting my computing preferences to the following:

Use no more than 25% of the CPUs,
50% of the time,
with 'in use' meaning input in the last 1 minute,
and to suspend when CPU usage is over 35%,

then setting BOINC to run based on preferences, BOINC will never run. All tasks are listed as being suspended because the computer is in use.

I decided I didn't really want to put the time and effort into solving the problem and simply uninstalled the program, but now I am forced to solve either this problem or the next one.

Problem 2: After uninstalling BOINC, on my next reboot, BOINC runs at full speed, with no way to shut it down. It is not listed in System Monitor under preferences, but I found it through 'top' and killed it there, though. It resumes on the next reboot.

Any fix for either problem here?

While waiting for a pro answer from somebody else, it might be interesting to see if a development version here might solve those problems:
https://launchpad.net/~costamagnagianfranco/+archive/ubuntu/boinc

Checking for the last time there was user input has been a problem area in BOINC for a long time. I can't remember if 7.6.31 is one of the buggy versions. There is newer version available from the PPA mentioned if you are interested in trying it.

You probably still have "boinc-client" package installed. BOINC client is the program that downloads, starts and reports tasks. Manager is just a program that shows what the client is doing.