Altium Designer 3D collision/distance problem
It sounds like your vertical component clearance is set to infinite, or at least a ridiculous number. I generally set mine to 0mm unless a specific application requires that I change it. You can modify this value in the Design -> Rules window (shortcut D-R), down near  the bottom under "Placement". Look for "Component Clearance" and set the "Minimum Vertical Clearance" to 0mm. If the radio button to the left is set to "Infinite" you'll have to change it to "Specified" before adjusting the number. See if that helps.