This problem was found by Robin and took us a while to find what was going on. What happens is that when you use checkpath, and you don't pass _any_ --owner option, it assumes EUID/GUID pair is what you want to set it to, which in most cases is 0:0. Now this would be okay _but_ in this case we have a problem as the old munin-node pid file was created in /var/run/munin — which has to be owned by munin:munin. But since munin-node is run as root, it has no -o option. So what happens is that /var/run/munin is changed to be owned by root:root. Confusing? Quite a bit. I'd suggest skipping over the whole owner check unless an explicit --owner is passed.
This has been fixed by commit 6f345ab.
(In reply to comment #1) on a semi-related note, you should assign "true" and "false" to bool types, not "0" and "1".