it's the setup ... probably
Your fences may not be long enough to prevent a small variation in the edge. The longer the fence on a router table and the table saw and the longer the jointer tables the better.
If that's all the equipment you have available, I would just use a hand plane to remove a touch on both ends and see if that helps with the issue.
A 48" aluminum carpenter's level makes a pretty good straight edge reference tool. If you have one, see if the gap you mentioned shows up.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)