Several OOTB queries cannot be copied/modified because they contain special, seceret and very, very useful criteria which are hidden. Like 'all groups I am a member of'. So while that might explain the odd query, like workload, I wouldn't have thought it would cover notes as well. I suspect there may be more than one issue.
Personally I found we had to re-write almost every system delievred query to have things like the sort order right, so I'd bite the bullet and create new ones.
Strange thing is I couldn't delete them either, even if I wanted too.