The calendar is a neglected feature. Hopefully it will receive some love and care for version 3. At the very least it needs to support iCal and recurring events. The general admin page would have been my first port of call too. I can tell you that those settings do effect modules, but you're right it should probably be a site-wide setting.
I'm no expert on the term "semester" but I believe it varies from college (university) to college but generally implies one continuous period of academic study which might typically run from the end of August to the middle of December and then again from the end of January to the middle of May, creating an entire academic year (and ignoring Winter and Summer semesters, as they are generally held over a much shorter period and allow people to make up for extra classes they need or to graduate early).