Joe, while I do not have access to the logs on my dedicated server right now (maintenance mode) I can tell you what the setup is because this seems to be a thing for us also. After we kill enough zombies in an area, you can hang out all day and see maybe one or two wandering around. I am on Navezgane, default configuration minus an experience boost I am running for new players right now. There are no warnings or errors in my logs minus one about disabling HDR on reflections, which is silly because it's a dedicated server, not a client hosting.
I can get you the logs in a bit, but without errors or warnings I doubt they will help you much. You are also more than welcome to pop on and check it out sometime. I can set you up with admin should you need it.
Actually the server just finished and is rebooting. Looking at the last log I see issues with the logging itself. I was logging an oil-shale vein near my base. I gained multiple levels. However, each time I leveled it said XP from killing/harvesting/whatever was all zero. That isn't true. I harvested close to 40,000 shale and with the experience boost it made me level four or five times. I'll post the log online.
Dedicated Server Log
Again, they spawn in areas we have not been before, but it seems as though, even on next to max difficulty, they don't repopulate areas we cleaned. If they do, it isn't very quickly.