Thank you for your replies. It's helpful to read other opinions.
I'm not new to building PCs, but this is my first Core i7 system, first system with an aluminum case, and first case with a removable motherboard tray.
Yes I'm using the I/O backplate shield that came with the motherboard. I can't say the shield is perfect by any means, if I hold it against the back of the board (all outside of the case), some of the USB ports are centered, some sit off to the upper-right.
I used the standoffs that were provided in the Lian-Li A17 packaging, nine of them per the holes in this board. They are stainless steel from the looks of it, not brass. All holes in the board have a matching standoff on the motherboard tray.
Well I fixed it, I suppose. I originally had the case on its side, and try after try I'd take the board and carefully lower it onto the case motherboard tray, then slide it towards the back of the case so the ports poke through the I/O backplate shield. Every single time I'd look at the back, the left ports would be alright, but some of the ports on the right would sit low down. Now this is with small copper washers under the metal standoffs, bought from Ace Hardware. No way would this board line up with just the standoffs.
So after it still not lining up, one of the posters here mentioned warping or bending of the motherboard tray. So I decided to sit the case upright, and for the first time take out the motherboard tray, attach the board to the tray, then carefully put the tray + board into the case. Do you know, all ports lined up *perfectly*! I'm sitting here not knowing exactly why I'm successful with this, I have a "who cares, it works now" attitude, but I still can't think what the issue was, maybe the tray wasn't screwed in from the factory.
I still needed the copper washers though, otherwise the board would not have fitted or aligned correctly, it would have been too low down. It still would have fitted into the I/O backplate shield, but almost none of the ports would have been functional. I also had to shift the board to the right slightly when I screwed it into the tray. I also checked that a graphics card can slot in without needing a spacer under its bracket, all seems fine. Odd. First time I've experienced this type of issue.
Thanks.