See the first screenshot:
I have 4 strips to be rendered in four parts of the screen. The problem is with the lower left one (with the two guys, one with a white shirt and another with a green T-shirt [me]). On the VSE preview (top-middle of the screenshot, it is perfect. It renders perfectly as well when I render at 100% resolution.
On the right of the screenshot (within blender), rendered at 50%, only part of this image is visible as it is shifted.
On the top-left of the screenshot (the "URL - KMPlayer" window), it is rendered at 25% and completely shifted (out of the screen maybe).
The screenshot shows that the transform is quite complex as I needed a well-positioned crop (hence the offset), then scale, then move the result (hence the position values). And you'll notice I first flipped on x.
However, on the underliying strip ("Robert guide 2"), I used no offset, crop, nor flip (you cannot see this in the screenshot).

On the 3 other parts of the scene, I used only some of those techniques to crop/shift/move the small strips. So this is really the combination of all of those that create the problem.

On the second screenshot: problem is the reverse: the shift is in the preview (top left) when rendering engin is set to render at less than 100%, but there is no shift on the render output (bottom right), whaterver the resolution.

The bug in the second screenshot is a small annoyance, workaround being to set 100% resolution when you position the bits. The bug in the first screenshot prevents correct rendering at less than 100% so is pretty much annoying.
1st example is on movie strip, 2nd on image sequence.

Using plain Blender 2.64.0 r51232 (dowloaded from Blender website) on Kubuntu 11.04, 64 bits.

Mayeul

PS: the blender file itself is 30MB (without any of the images); that would require a lot of cleanup to reduce it to something uploadable, I may try if nobody can reproduce.