Hmm, I'm really at a loss for why you're seeing that result. Can you try some of the following and see if they have any effect?
1. Reinstall the bookmarklet. Delete it and go back to www.boxee.tv/watchlater/alpha
and re-add the bookmarklet. Is there any chance the machines with the issue had the bookmarklet installed from staging or some other non-prod environment?
2. Use the cache-deleting tools in IE9. Maybe something is getting cached when it shouldn't be that is making the browser thing the user is still not logged in?
3. Open up the developer tools console (F12) and look at the "Console" tab... any error messages?
Not sure if any of these will shed light or not...