Eddie - I had what sounds like the same problem, will she start OK but you can't engage Neutral button?
1. - could be a bad throttle, there was a recal on some Mercury 3000 models last year, you may be able to check with Craig Roberts (look in the member list) from Tracker MI.
2. They may have just mis-alligned the shift linkage. Last time I had my tracker in for service this happened. I could NOT engage the neutral bottom in when running, OR when out of the water could not engage it either. The boat would start but would be engaged in Forward. Took it back to Tracker and they in a matter of 60 seconds re-alligned the shift cable and off I went!