I would check the error log for any clues, maybe file permissions are not right. /Data/currentlog.config is the log file.
If it doesn't run the scripts it usually means they are missing but it could also mean it can't read the files.
But really if it says your system is up to date it sounds like it is not really running the latest code as you think it is. Maybe you had deployment errors and it did not upload the newest dlls in the /bin folder