Found the problem. Harvesters, Battleships and Supply Ships are all 3-level UFOs, that is, their map blocks are 4 levels high (Ground, 1st floor, 2nd floor, roof). As the deployments in the ruleset specify the default 4 level high battlescape and my map blocks have an underground level there are only 3 levels for squeezing in UFOs. Changing all the height values in the deployment definitions to 5 fixes it.