hmmm... im assuming you mean whenever you open a program that puts an icon in the system tray... do all the programs that run on startup get added to the systray correctly?

possible solution - have you ever installed desktopx? check your list of running processes to see if there is one called trayserver.exe, and if there is, use msconfig to disable it.

also, check your themevars.rc to make sure that scripting is turned on, the systray wont autosize if it is turned off.