I think it may be as simple as adding -minimized after the run command (leave a space before the -minimized). I think I have seen this somewhere before, but can't be certain if it was -minimized or - minimized.
However, as Bob mentions, what is it you are trying to minimize and why ?
Most programs that start on boot (exceptions in msconfig, startup tab) that I have seen in the past tend to be running in the background or system tray or are services, etc.
Many programs in their settings have an option to minimise to the system tray.