Shifting Priorities - The Foundation's mission is consistent, but constant revisions to projects and priorities creates a never-ending feeling of start/stop, re-org, starting new work, end work, sometimes restarting etc.
Experts as managers - Bringing 'field' experts (educational or medical) in to act as managers...when that is not really their skill sets creates unrealistic expectations and sometimes poor management situations.
Technology - with as much endowment as the foundation has one is always surprised at how poor/outdated their overall technology is (financial, Data, Grant Management etc.)
