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1. Off-by-one pixel coordinates
2. Sampling of wrong pixels at some non-integer stretch factors
First was noticed while comparing screenshots of the software and opengl w/glsl renderers (opengl output was shifted up and to the right). Fixed by subtracting a 1/2 pixel from the texture coordinates when calculating the bottom left pixel to use for interpolation.
Second was apparent when running pac-man fullscreen on a 1920x1080 screen and allowing non-integer stretching. Manifested as irregular horizontal 'steps' in the output. Fixed by sampling from the center of all pixels which should avoid any funny business in regards to pixel coordinate rounding.
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