It's within that script tag... you have {$milestone_url} and I suppose your script just appends the project id at the end, but a "/" ("%2F") is needed at the end of {$milestone_url}
I am also having issues - I've got 0.3.6 and it installed fine, but I can't see anything other than the dashboard, no matter what URL I try from the one on your blog post or the ones written in here...
I was being dumb - After I finally configured everything right I didn't see the admin interface section, and hadn't enabled it. Working now, thanks very much!
I've released and uploaded a version for those, who were using Active Collab installations with urls via path_info (like kaitlyn2004) . Now it should work for all :)