You can see Edge playing his 1967 Fireglo Rickenbacker 330 12-string in some shots and a Jetglo (black) Rickenbacker 360 in other shots.
The difference being that they were shot from different shows.
U2 played Boston 4 nights. June 05, 06, 08 & 09, 2001. Boston, MA at Fleet Center. I think the filming was from nights 3 & 4.
The issue was that Edge thought they killed the song/played it horribly. In the footage, you see Edge throw his Fireglo finsh Ric to the ground and then come back and kick it. He damaged it and hence the Jetglo (black) Ric 360 12-string was used the next night.
In fact, they'd even called out to Boston GuitarWorks to see about borrowing a Fireglo 330 12-string so that the filming would have continuity. Boston Guitarworks didn't have a mid-60's 330 12-string but did send over a 64 reissue 360, similar to the one George Harrison used. (Original 360's were the same shape as 330's but with white binding). In the end, Edge didn't use the guitar that Boston GuitarWorks sent over but DID autograph it for them. Boston GuitarWorks had it on thier website for a few years, listed at around $4,600.00 (if memory serves). They must have eventually sold it as I don't see it on their site now.
For those complaining that U2 are very careful about what it released to the public, I thought it was honest and refreshing that they left that in -- Edge sort of losing it for a minute. It's almost funny, I mean to throw it down is one thing but to then come back and kick it?!?!
If you watch the alternate camera angles, you see Edge go up to Larry after the tune and he's yelling something at him. I'm pretty sure he's not saying "nice job".
YouTube - U2 - Gone live from Boston