For anyone running into a problem where build automatically is unchecked but the project is still building. Make sure your project isn't deployed to the server in the server tab and told to stay synchronous.
You can switch to manual build so can control when this is done. Just make sure that Project > Build Automatically
from the main menu is unchecked.
if needed programmatic from a PDE or JDT code:
public static void setWorkspaceAutoBuild(boolean flag) throws CoreException
{
IWorkspace workspace = ResourcesPlugin.getWorkspace();
final IWorkspaceDescription description = workspace.getDescription();
description.setAutoBuilding(flag);
workspace.setDescription(description);
}
Source: Stackoverflow.com