My current setup involves two blue div elements connected by jsPlumb. You can view the setup here: https://jsfiddle.net/b6phv6dk/1/
The source div is nested within a third black div that is positioned 100px from the top using position: absolute;.
It appears that jsPlumb calculates the connection based on the difference in position between the black div and the blue source div (which is 0px). This means that the target endpoint is drawn according to the absolute positioning of the blue source div. If the blue source div were at global coordinates 0px, 0px, the target endpoint would be aligned correctly:
When I remove the position: absolute; from the black div, the target endpoint is positioned correctly. However, my setup requires nested div elements to maintain their relative positions to each other using:
.item {
position: absolute;
top: value;
left: value
}