I've scheduled a script to run under my username. If I'm logged on when the script runs, a command window pops up and disrupts my work.

If you schedule a task in your own user context, this situation will occur. The best solution is to schedule all tasks to run under a special user account that you use like a domain service account. If you administer the domain, adding a new user and granting this user the permissions needed to run the scripts and access other server resources is usually easy. If a special user account isn't an option because of domain policies, the Task Scheduler could launch a single-line script like the following to start the task script in minimized form:

START /MIN
  C:\scripts\newscript.bat