When interlacing, every half-frame is the "current" frame, so if you start counting at a certain time index, then every half-frame is "half a frame" further in time. The reason why you see it "perfect" on an interlaced output is that you always see the current frame. It's a result of the flickering: You miss the steady picture and only get the current information.
Indivision AGA MK2 does what *all* flickerfixers have done in the past: It composes a progressive-scan picture from the last two half-frames.
Naturally, these two interleaved half-frames belong to a different time-index, so the resulting picture is a mix of the "current" time-index, and "half a frame ago". There is no "clean" way around that, as demolition already mentioned. In essence, you trade the flickering for the interlace artefacts. Since these artefacts only appear on horizontal movements and ONLY on interlaced pictures (which are hardly ever used in games), I'd say that's a good compromise.