As others have said, the throttle and transmission linkages are independently adjustable. Hard to say what needs to be adjusted, but one or the other. As Daydreamer mentioned, there is also a button to the transmission linkage for starting the boat (when you want to give it some throttle, but don't want the boat in gear). If I remember on my Hunter280 that had the single lever throttle/tranny, i had to be in neutral to use the bottom (could not disengage while in gear...which makes sense I guess).
Look for an instruction manual for your specific throttle control (you did not tell us what manufacturer / model it is). I believe you can adjust at the throttle control, and you can certainly adjust the linkage at the tranny and engine throttle. I just don't know for sure what you need to do to fix it.
Sounds like an important thing to sort out though! Don't want to coming into a slip at WOT to keep her in gear, or having the tranny drop out of gear when you need it.
Good luck with your project. Let us know what sort of throttle control you have.
Greg
