I have short shocks on my wife's 550 and I find it best to adjust it with the weight on the back tire, as the new position puts the swingarm right at the apex of movent, so any further upward movement can actually slacken the chain. (I think HondaMan made a comment about having to adjust the chain a bit tighter than normal because of this, might check with him...)
Sometimes if I go over a sharp bump it will slacken the chain to the point where it whacks the stamped chain guide behind the front sprocket cover, making a "ping" sound that's hard to track down...