Okay, I've just had something strange happen. Doing a new film, the first strip seemed to batch scan absolutely fine - with no frame offset problems. The second strip had the problems I've been having, where the first frame was okay, and the second slightly out, and so on.
However, by pure chance I noticed that I'd put the first strip into the LS-40 'face down', and the second 'face up'. So for some reason I tried the second strip face-down, and turning the film over seemed to solve the problem!!! Any clues as to why this might be happening? Am I completely missing something fundemental?! Thanks Mark