When I try to enter automation data in the main project window, sometimes Cubase won’t let me. When I click using the pencil, an automation data point will appear but then disappear after I let go of the mouse button.
Just some thoughts, make sure snap is off and you are not zoomed way in. You might try opening the automation panel, then lower left click on automation settings, and make sure the reduction level isn’t wacky. Mine is set to 50.
Really this sounds like you are first changing your tool from the arrow to the draw tool and that is what happens if you do that…the automation data point appears while you hold down the draw tool, but the vanishes as soon as you let go.
You are trying too hard.
Just use the arrow tool in the automation lane and it should automatically change to the draw tool when you touch an automation line. Then proceed as normal.