Have you disconnected the cable and tried shifting manually with the lever on the transmission? If things go well then, perhaps your cockpit lever is limited somehow in 'throw', making it difficult to fully engage the gear position. The cable will only reproduce the motion of the shifter..
Also make sure that the clamps on the cable are secure (both ends) so that you don't have any 'lost motion' in the assembly.
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)