The reason behind your problem (a speculation until you provide me with an answer how you installed the Agent) is that in every update the agent recompiles it’s components (local build). If you install the Agent with the 2 first methods you would not even notice any activity between updates.
Since you’re on a Debian system, I suggest you do a full uninstall and then install again with kickstart.sh. It will default to use our binary packages, which will eliminate the CPU/Mem spike. If you have user configurations under /etc/netdata, keep those files somewhere before you uninstall, so you can add them again after the new installation.
We’re a bit cautious to not mess up custom installations, so the previous installation type is used to guide kickstart in deciding whether we can use binary packages or not. In your case we can’t.