do you have a special tray utility or multiple desktop utility?
if you uncheck the "start minimized" option, does it start normally and then let you minimize it to the tray manually?
I unchecked the "start minimized" option, rebooted, and found after the program loaded that it no longer appeared on the taskbar but also didn't request minimization to the tray, and that the system tray icon was still invisible.
I run XP Home SP2 BTW, and I've noticed that sometimes, although startup programs load, their icons don't appear in the tray.
What's odd about SC's behavior is its invisible tray icon. Somtimes it appears and sometimes it doesn't but there's always space reserved for it in the tray.