System Usage - Meaning

I gathered it means memory – thanks to running into some memory outage errors that had me restart the VPS a few times over.

Coming to the next question: Why doesn't memory usage come down after running memory intensive scripts?
I would get a black X beside system usage even if we only have like 40% to 64% beside the System graph. Wonder what it means?

There was one time, though, that the black X disappeared when I restarted mysqld. Wonder if its because my mysqld is not "optimized?" Any suggestions?

Black "X" will be shown in VZPP in case if resource overusage attempt was detected within last 10-15 minutes. "X" will be cleared out if no alerts were logged within last 15 minutes.