I've noticed that in FSX, you can either fly a hair below the glideslope indication on the HUD, to get a 3-wire, or fly right on it, and get a 4-wire every time. If you fly the Ball, you will get a 3-wire, but the LSO's will call you a little low in the groove. You can do one or the other, depends on what you're trying to do. Hit the 3-wire with a slightly less than perfect grade by the vLSO's, or get a 4-wire with no vLSO comments. Assuming all other factors are correct, of course.
It may be that since the T-45C is a trainer, the LSO's are a little harder on you than for an F-18? That may be why it's harder to get an OK pass. Just a possibility. Or maybe the LSO program is optimized for the faster F-18, and the T-45C has to be flown slightly differently than it should be to get an OK.
Just a couple of my thoughts. I may be totally out in left field on all this, though...
Pat☺