I am apparently the only one on here that has experienced this, but when I bought an older model year soft top takeoff for my 2013 JKU, I had an interference between the header and the center footman loop. There is a cutout in the header to clear the footman loop, but the position of this loop apparently changed an inch or two at some point. Newer tops have a wider cutout in the header to clear both loop positions, but the older ones do not. It's not much of an interference, but enough to keep the top from sealing completely.
I think the top I bought was supposed to be an 09 takeoff, but I can't tell you that for sure.