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When I purchased my car the window would only go down midway. I figured it was an motor issue so I bought a new one. That didn't solve the problem so I checked the window guides and found the front lower was bent severely. I ordered a new one just installed it window now goes up and down no issues. (besides when it gets to full close it comes back down. Well I went to shut the door and it sprung back, I now know how the first guide was damaged. Has anyone else experienced this? I just left it unbolted for now.
What year is your car, and which window is having the problem? If this happened to just one door, I would look and compare with the other door to see why.
The "Detend Rod" you mentioned should be encased in a casing/pocket called "Door Check" (see circled in red). If the rod is out of this Door Check, or if the Door Check is missing, the rod will make contact with the window rail.