Are your daemons running? That will explain the part about "not closing revisions", and it might also effect the lint/unit "run" not being complete.

This is strange. After you mentioned daemon, I log into the admin account and see an issue about daemons not running. However, when I ssh to server and run the demon, it told me that demon is already running...

Here is the screen shot.

You can use 'phd restart' to stop all daemons before starting new daemons.

I tried yesterday, with phd restart and it doesn't work. it restarted the daemon, but on web the issue still exists. Then I restart the whole server and the problem is still the same. Today when I wake up, I restart the server again. Magically the problem solved. I don't know what's happening here but I will close this question for now. Thanks avivey for your help here.