"Apocalypse Now" is an example of that. I first saw it in my teens. Subsequent repeat viewings, I've appreciated it a shitload more than the first time.I'll have to give it another go. It was at least 15 years ago that I saw it. I'd say by the end I was just completely disengaged.
I have found a few movies that I thought were rubbish on the first viewing be much better second time around. I think that the second watch their are no preconceived ideas on what it's about, so expectation doesn't lead to disappointment. No Country For Old Men is a classic example of this for me. I saw it at the drive in when it came out and thought it was shit. After years of reading people rate it so highly I gave it another go a few years ago and really liked it. I think first time around I was expecting a classic western style type thing. lol
The most extreme example that comes to mind is "A Clockwork Orange". The first time I watched it, I didn't even complete it....did not like it. I would have seen it three more times since then over the years...last time was sometime last year and I really appreciated it as a great film. Probably the first time I truly got what the film was trying to say...lol.