Jens,
There's knocks, and then there's knocks. They don't all sound the same and they all have different causes.
A 'roid can knock from a number of causes:
1. Loose or ill-fitting gib keys can cause the flywheel to rock back and forth on the crankshaft, taking up hard against the sides of the gib key with each power stroke and compression stroke. Sounds just like rod knock. My engine had it. It took me almost a year to track it down to poorly fitting gib keys and keyways in the crankshaft that didn't match the width of the keyways in the flywheels (Ashwamegh engine). Brass shims solved my problem.
2. Rod knock. Loose or worn big end bearings are the usual cause. Shouldn't be any problem in a new engine with 0.002" to 0.005" or thereabouts clearance.
3. Timing gear backlash. Probably the biggest source of mechanical noise in these engines, and the most difficult to fix. This is an ongoing subject of discussion, and about the only way it can be fixed is by fitting an offset idler gear spindle. Dave (Xyzer) seems to have pretty well nailed down that solution. A number of folks have carefully measured the backlash in the timing gear train and found it to be excessive. But it varies engine-to-engine. Some engines absolutely rattle (my Ashwamegh 6/1 does), while others like the Beta Test engine were about right out of the crate. .
4. [EDIT: Detonation] Pre-ignition. Can have a few causes:
a. Depending on where your engine is injecting its fuel charge, you might have detonation pre-ignition. [I'll admit this is more applicable to gas engines than diesel, but I thought it was funny, so I stand by it by virtue of artistic license] Sort of like that embarrassing male problem that all of us have heard sometimes happens to other guys, but never to ourselves, if the charge is injected before when the conditions are not optimal, the results can be disappointment. And if left untreated, engine damage can occur.
b. Pre-ignition Detonation can also be caused by burning fuel with the wrong cetane rating. Rather than burning, which is a smooth, relatively slow and controlled process, the fuel charge can detonate, literally exploding in a chaotic blast. Try burning white gas (lantern fuel) in your motorcycle and you'll hear what it sounds like (don't ask me how I know!).
c. Pre-ignition Detonation can also be caused by an overheated engine. I mean overheated to the point of near destruction (don't ask me how I know!).
So to say simply that your engine is making a knocking sound doesn't tell anyone very much because the causes can be so diverse.
Hope this helps.
[RAB makes a very valid point about the distinction between pre-ignition and detonation, which I'm aware of, but got sidetracked in writing the above. They are both bad things for an engine, and indicate that the engine needs attention. And, yes, 0.005" is too much slop on a new engine but you might find that kind of clearance in an old engine, especially one run on heavier lube oil to keep it quiet. And, yes, IDI engines are quieter and have a different sound than a DI engine, but I thought we're all talking of IDI Listeroids here.]
Quinn