Notification area icons are sometimes invisible in Windows 7 (Boot Camp)
What I did to fix this was disconnect the Ethernet cable from my iMac, and when installing Windows 7, don't connect to wifi just yet. Then, install all Boot Camp drivers, and only then can I reconnect Ethernet and wifi. This prevents Windows 7 from automatically downloading drivers when it is unable to communicate with the iMac's features, since the Boot Camp drivers were not initially installed.

So, the notification area problem seems to somehow be related to conflicting Windows 7 and Boot Camp drivers. I notice the problem briefly returns when I install Windows 7 updates, so that seems to prove my point.