If you don't need to deliver tape, you might find it still works OK in a QT movie or web stream if the problem is that it's just dropping frames. Is the message to warn you showing up or have you turned off the warning? Just sounds to me like dropping frames.
That said, what codec is the timeline set to be and what codec is this footage that stutters? Do they match? If not, you might try transcoding the source to the same codec and frame rate etc that the sequence is set to. DV? or?
Next question is what are you using as the scratch disk for the source footage? Shouldn't be your startup disk.