There's an (I think) well known bug where trying to use a newer boincmgr to pause or abort work on a much older version (it happens to me where the remote system is running 6.10.58) just doesn't work. The command is ignored by the older system. During the recent LLR testing, I was trying to get both an SR5 +1 and SR5 -1 on a 6.10.58 version of BOINC running on a non-GUI linux. There are twice as many -1 job, so I had to keep aborting until I got a +1. I could not affect tasks with the GUI on another machine in any way. I wound up having to use the command-line boinccmd.exe locally to cancel tasks on the other computer. I could of course have used the same command line on the remote computer, but except for the --host portion it would have been exactly the same command.
If you're encountering that same bug, you won't be able to remotely pause any kind of job, LLR included, unless you're doing it from the actual machine where the work is running. They do not show as paused in the GUI, it's as if the abort command had never been given. I had to use:
boinccmd --host HOST_NAME_HERE --task http://www.primegrid.com/ RESULT_NAME_HERE abort
to kill the unwanted jobs. Other commands besides abort are suspend and resume.