check your blend mode
... the line tools...All of a sudden my line tools have a transparency to them. But when I click on the stroke the Opacity box at the top still says 100%.
What is the Stroke Weight?
Do the paths have Fill and Stroke (bottom of the Toolbox)?
A screenshot may help the helpers, especially if uploaded using the Camera icon to avoid queueing.
Open the appearance panel and select your line in the document window and see if you have a effect applied.