I had an issue with my Kubota wheel loader. Thought I was in for a world of hurt and expense. I actually didn't use it for a month or two fearing the worst. I even added Sea Foam to the crankcase to no avail and tried loosening every injector line to find a problem cylinder. Finally crawed under the machine only to find a bolt loose that holds the exhaust bracket! Talk about relieved!
Diesels are funny. Like the other post said, at certain RPM they can create harmonics. Sometimes for no particular reason, sitting at a light, my plastic dash on my Duramax starts to Vibrate.
Every dam thing on my Steiner Diesel vibrates at low idle making it sound like a piece of junk. A litte higher RPM and it's fine!