Thumping noise audible from the exhaust is usually from a valve being open/stuck at the wrong time. Thumping out the intake is usually from exhaust valve not opening, out the exhaust can indicate intake valve not opening or barely opening . I would think you would have very low if not any compression on the offending cylinder though. All rockers move the same on all cylinders?? Have you measured the rocker travel with a dial indicator to be sure?
Is it possible you didn’t have a pushrod seated correctly when you torqued the rockers down?
Is it possible you didn’t have a pushrod seated correctly when you torqued the rockers down?