I’ve been using OG since 2013, and am currently on version 6.6.2. Mac is on Sierra 10.12.3. I use OG to make wiring diagrams, and use orthogonal lines extensively. I have been using the same template (with tweaks here and there) for a long time, but one thing I cannot figure out is when my line behavior changed. I recall having X/Y control over the lines previously, but now I’m stuck with one direction of adjustment. I’ve searched here, and extensively with Google, and cannot find where to change this behavior in my version of OG (I only found a reference to the change in 5.3). Where can I change this? I even tried a new document and the line behavior persisted.
If you want to change the line itself but are happy with where they attach to the shapes, add/remove midpoints & then select them to move them to exactly where you want them to be or change the direction. If the problem is where the lines connect to the shapes on either end, the magnet tool is what you want to use to specify exactly where the line should connect to the object.
This post may be helpful to adjust to the way lines are handled in OmniGraffle 6 and higher https://discourse-test.omnigroup.com/t/newbie-question-dragging-orthogonal-line-segments/26711/2.