In order to have compression, the engine must first bring in a charge of air/fuel mixture to compress. With both valves closed, the engine CANNOT bring in air or fuel. Also, there CANNOT be manifold vacuum with intake valve closed.
Regarding possible problem with valve timing, NOT LIKELY!! In order to have a p[roblem with valve timing, the engine would have to have been disassembled to quite a bit more than you have described.
An engine is basically an air pump. Intake valve opens, and piston travels downward to draw in a fuel/air charge. Valve closes, and charge is compressed. At some point near top center, spark is provided by ignition system, and mixture is burned causing piston to travel downwards on power stroke.
NOW, using deductive reasoning, does it not follow that if pushrods are removed, and valves remain closed, the cycle is disrupted? You need to have the pushrods installed, valves adjusted, and correct engine rotation to evaluate possible problem with compression.