I searched through the forums and found some articles that made mention of this problem being solved by updating to the latest stable indie build, which I have done. However, some of the applications are still not appearing in the system tray. Specifically,

Miranda IM
Apache ( The Monitor )
Direct Update ( for http://www.dyndns.com )
Internet Connection Manager

I'm using the stock theme, Simplicity, the one packaged with LiteStep.

TIA,