Yeah exactly. I actually found a full manual pdf for the original 488. I followed the instructions carefully for dubbing track 2 over track 1, and still hear nothing from track 2 when I play it back.
Actually, that's a kind of great effect {or at least, it could be}, if somewhat unwanted !! I have had situations where I've wiped the track clean and can hear a faint ghost of what was there before wiping.
I think maybe you have a defective track 2. If you can get the machine serviced, then that would be the thing to do. Is it brand new ?
It doesn't sound as if you're doing anything wrong in your recording steps.
I remember back in early '93 when I'd had my 488 only for about two or three months, I did a session with some kids that I did a project with and one of them was a flute player. On the tune we did, I got her to do a part written, part improvised bit and the first take was great. I could see the bars lighting up to where I wanted them, but when we listened to it, it was really quiet, only one or two bars. So I got her to do it again. Same thing happened. In the end, I got her to record two passes and they were 'adequate', nowhere near as inspiring as the original take. I blended them to get the volume. It was my track 1 that was up the creek. Anyway, I got it looked at soon after and when it came back, it was perfect. Didn't have that particular hassle for years after and when it cropped up, a cleaning did the biz. I've been rabid about cleaning from day one - I clean up before each session and after each session and sometimes in the middle of a long session.
The Maddog said not to degmagnetize unless you know what you're doing. Good advice, but one
should learn what to do. It's not hard at all. You don't need to turn the 488 on, press the on button on the degausser from about a foot away and bring it very slowly to the heads and work the tip around without actually touching the heads if you can. It doesn't matter if you touch it slightly. Withdraw very slowly with the on button still on and when you're a foot or so away, then switch it off. As an aside, I've been doing this for over 15 years. But I'm not technical and I haven't got a clue what demagnetizing does or whether it's any good !

All I know is that I've never had any head hassles since I started using a degausser.
As for not using isopropyl on the rubber pinch roller, this is the standard advice given and I'm not going to contradict it because I'm not qualified in any way to do so and I don't want to give lousy or dangerous advice. But I've been using it on the rubber roller since 1993 and I've never had any problem with it. I've done {and continue to do} hundreds of sessions with the 488.