Ed,
I had a problem similar to yours at one point, I could configure my shifting so that forward worked perfectly, but going in reverse did not. It would "almost" shift into reverse. Sometimes it worked, sometimes it didn't. I was able to fix this by adjusting my shifting in "reverse" so to speak. Inotherwords, I adjusted my shifting so that reverse worked first, and then tweaked it so that forward worked. This worked fine for a few years, until I had a shift boot rip and decided to replace the whole shifting setup since it was old and seemed kind of stiff anyway. I found that once I put in all new shift cables etc, much to my surprise everything configured like you are supposed to by how the manual states and chris and others state. In retrospect I think I had a cable that was a little stretched, a slightly worn shift spool (and still do, it's a 1986 outdrive !), and crud in my lines making things stiff.
So like Chris said, I think you have something configured wrong. If you can't shift it by hand (pulling and pushing the cable) successfully (locking in reverse and forward and checking prop), you will never get it to work mechanically correctly.