I'm very sorry about this, Kevin. I'm working on the timer trying to get it in better shape, but it still needs some work. I'll announce here when I really think it's ready. For now, yes, that appears to be one of its biggest problems - I'd avoid using the timer on the site for events that take more than a few minutes, since it might time out on you and you could lose your times like this.I'm still having issues with the site. I just did 7x7x7, using the timer on the site, but after I hit submit and went back to the main page, my results are nowhere. I think it may be related to the time elapsed between login and clicking submit, but I'm not sure. Either way, it would be much nicer if you could stay logged in permanently, just like you can on the forums.
(Thanks for fixing multi to allow DNF results.)
I do hope to try to fix that problem - perhaps this weekend I'll be able to get to it. I'm not sure whether I'll be able to let it stay logged in or not, but at the very least I want to make sure your times are not lost completely when it times out.