"An Cat Dubh" and "Into The Heart," so you know, are supposed to bleed together; they're really one slightly longer piece. That is intentional.
As for the whole "One Tree Hill"/"Exit" deal...well, yeah. It's ALWAYS been a problem. From what I've been able to discern simply by listening to various versions of the album owned by various people and purchased at various points in time, earlier pressings of the CD seem to be pretty much okay. A great deal, though (from the '90s, as far as I can tell), seem to be fucked up. Post-Pop versions (literally every single one I've encountered) have been perfectly fine.
Now, I've only listened to like ten or so different copies of the album, so I could be totally wrong. TOTALLY wrong. Still, that's what I've been able to discern. The vinyl versions being jived up is news to me, though--I find that fascinating and, at once, unforgivable. Madness, I say.