If the projects are being submitted separately, the separate LEED boundary for each project takes priority.
Although it's tempting to delineate the responsibilities by who's the contractor, it's more important for the site boundary, performance, materials, and credits to be a logical whole for each project submission even if it means having documentation provided by more than one contractor for each given project. We've often been reminded that a projects LEED site boundary "must be defined consistently for all credits."
If I understand your situation correctly, the parking lot adjacent to the barracks that serves the dining facility should probably be made part of the LEED site boundary for the dining hall. All the parking spaces, heat island areas, construction waste, regional materials, and recycled content within that boundary needs to be applied to the Dining facility, even if two different contractors do the work.
The Application Guide for Multiple Buildings and Campuses has not been updated yet for 2009 versions, but the earlier version can often apply in these situations. Do take a look at it, but I don't think it's guidance would steer you in a different direction.
Hope that helps.