Version: 2.54 Build r31878
In the Sequence Editor, the connection between effect and keyframe curves can be seriously broken by moving the input channel via numeric input.

No BLEND file (this is easy to repro).

Reproduction steps:
Go to Video Editing screen layout.
Add an image to a channel. Place the start at frame 1, and give it an extent of 50 frames.
Add a transform effect to the image.
Insert a keyframe at frame one on Uniform Scale, X-pos and Y-pos
Go to frame 50, change scale, xpos, ypos, and insert another keyframe on all 3. (you want to change them significantly so that you can easily see where the keyframes are in the timeline).
Now select the input channel (image), hit "G" and drag in the X axis (time). Note that the curves in the IPO window move along with the effect. Hit escape to cancel.

With the input channel (image) still selected, go to the properties window, and type a start frame of 60.

The input channel will move, but the effect channel will stay put, as will the curves. It is not updated even if you change selections, or add another input strip. This is the first problem.

Now hit "G" and move the input channel. The effect channel strip will snap to the position of the input channel, but where did the curves go? You can find them by mousing over the IPO window and hitting the "HOME" key. They have jumped to some random negative frame number (I've seen up to -21,000). This is the second problem.

If you subsequently drag the input channel, the effect channel and the keyframe curves will track it, but the curves will keep their time offset.

The Effect channel is also not updated if the duration of the input channel is manually entered, however it does not appear to harm the keyframe locations.