Hi
@Snowdogyyz:
Are using single coil pickups for cleans and humbuckers for the others? Because that alone would account for the discrepancy of what you describe above.
Use Scene 5 instead of Scene 1 for cleans with single coils. All the bank 1 and 2 presets "cleans" (scene 1) are leveled on the same pickup as Scenes 2-3-4 - usually the same bridge humbucker on my SG- same range. Sometimes (preset will say) I use the middle position or the neck humbucker. A single coil guitar (Strat, Tele) pickup general hits the amp roughly -5db less than a mid-focused humbucker.
If anything I level leads (Scene 4) a little louder than the other Scenes 1-3, because I level it playing at 10th fret, not low E and A chords.
I can promise you that most Scene 1s have same level on a Universal Audio console meter as Scenes 2 and 3, and not 60%/70% less. Keep in mind a clean is more dynamic than a hi-gain compressed amp. You can spike a signal (create spikes transients) a lot more on clean amps settings, and exceed the level on a clean amp sound than hitting them on a gainey amp that is compressing more. The Shiva Clean and Tweed Princeton are good examples of clans with a very dynamic level range based on how soft or hard you hit the strings for clean, I just aim to "average" between that to level those kinds of amp cleans.
Just turn up the the amp LEVEL if you want your cleans louder. But on my end they are leveled correctly. If i made them much hotter then they would spike levels up to -6db if I whack the strings, or if I added a drive block in front of them.
Hope that helps!