Yes, it appears the mystery was solved. Indeed, the single version I listened to is shorter than the 1989 Singles Collection version. I listened to them simultaneously to confirm this (the single version ran ever so slightly faster, but I blame that on my record player, the cassette deck I used to record it, the cassette deck I used to play it back, or a combination of all three - anyway, I compensated for that, so it didn't affect the result in any way). I can't tell for sure if it was a different mix (I'd have to listen to it in more detail), but it probably was.
But it's good to know that (as far as we can tell) that alternate version, while unavailable on CD, is not rare enough for me to feel bad about having thrown it away. Phew...