He said Apply Audio FX. Is it possible Cybertizzan is applying FX like when you choose Process > Apply Effect and it's going straight to the clip without going through the gain stage?
Cybertizzan, I don't usually use Apply Effect so I'm not much use. But I think it is possible that apply effect works differently than Freeze Track. Freeze Track actually bounces down the track and keeps it inline. I think that's what you're after here. Apply Effect is really limited to just the FX applied and the related clips.
If you want a new track with the FX applied to the wave form exactly as you have it, you can use bounce to tracks. It's not quite the same as Apply FX, but it might serve.
If your goal is just to free up processing power, you should use Freeze Track.