I am having this issue with mae free edition as well. Running windows 7 pro and firefox. No viruses, no recent registry changes. This happens at a couple of different websites. Last time was today at CNet.
In trying to solve this issue, I noticed that when turning off the browser and restarting it, the mae icon and startup message did not appear in systray taskbar. Opened mae, and it said it was running, but I don't think it really was. At least, it was not functioning. Clearing the cache, dumping all cookies, and restarting the computer does the trick. Until all three are performed, the icon does not appear in systray on firefox (or chrome) startup, even though mae says it's running.