Just a thought, but is it possible the users who are invisible are registered in a different time zone (utc -4) than the server is in? That would affect the log report because if you were looking for someone in a certain time frame, but they are in a different time zone than the report is looking at, then it might not show up.
I admit this is a longshot. If the logs are doing this, then it is a moodle bug, because reports ought to show the time users hit the server. But this is the only thing I can think of that might cause the symptoms you describe. Do let us know how you solve this, if you do.