I have this issue on several sites. It appears sometimes it will work and other times (usually most of the time) it just doesn't check the box to keep me logged in at the site. I've tried deleting and recreating the login making sure the box is indeed checked when I login and saving the new login. I log out. I come back to the site login and attempt to have 1Password to log me in while checking the box and it skips it again. If I'm lucky and the login takes a little longer than usual I'm able to check the box myself but most of the times as soon as 1Password auto submits the login credentials it takes me to the home page of that site and I'm unable to check the box manually. Again, this happens most of the time and other days it works fine.
This happens on both Safari and Firefox by the way. Here are the details you probably want:
Mac OS X 10.7.4
Safari 5.1.7 (7534.57.2)
1Password MAS Version 3.9.5 (39500.018)
1Password Safari Extension 3.9.4
1Password Firefox Extension 3.9.4