You'll want to give the MPR Supplemental Guidance document a close read, especially for MPR's #2 and #3, but nothing in your situation appears to preclude you from registering this as one LEED project. One construction schedule, one CM, one owner.... sounds like one project.
See http://www.usgbc.org/ShowFile.aspx?DocumentID=6473

The small size of each building is an especially compelling reason to treat this as a single project, as the soft costs for documentation can become a higher percentage of total project costs as the project size gets smaller. Anything you can do to streamline commissioning, materials tracking, documentation etc. will be worth doing.