This doesn't happen on all sites, and not all the time. But it happens frequently and unpredictably enough to make it VERY difficult to use Orion as my default.
Here's an example. Using .9-rc:
This seems to happen more frequently when trying to sign back in to a site after being logged out and on sites where a login is entered on one page and then a password entered on a second page.
Just now, I went to a site with this two-stage login. My userID populated with 1Password as expected on the first page. But after submitting that, the second page exhibited the same behavior in the movie above—clicking the one password icon in the password field did nothing, nor did attempting to fill from the toolbar button. (Nor did using the auto-fill keyboard shortcut work).