Also try throwing away the InDesign preference files.
It it that your pen tool isn't constrained by holding the shift key down when you're drawing lines? Or that when, having already drawn the line with the pen tool, you select it with the Direct Selection tool to shorten it, and line strays out of true?
If the first, then I don't know why it wouldn't work. If I place a point with the pen tool, then click a point anywhere near, say, 0, 45 or 90 degrees (with the shift key held down) I get a line at one of the those angles.
If you're simply trying to shorten an existing line that you created with the pen tool, and want it constrained, then the tool to use is the Selection tool, I believe, not the Direct Selection tool.
If you're trying to change the orientation of the line from, say, 90 to 0 degrees, then I think you're right, neither the Selection tool nor the Direct Selection tool will be constrained by the shift key; I beleive you'll need to use the transform palette to change the orientation precisely.
Don