Virtual Environment Compliance is for vCenter properties, Host properties, Guest container properties (e.g. resource allocations and reservations, copy and paste enabled, etc), and a variety of data from vCloud Director and vCloud Network and Security (formerly vShield).
Machine Compliance is for OS internal data from guests or physical machines, like file versions, service configuration, software installed, security policy data, registry data, patch status, and so on.
P.S. The main place these come together is when using VCM to report Compliance rollup information to vCenter Operations Manager. This is where a guest will have compliance data for it container properties and its OS internals aggregated into one Compliance Risk top level score.