EZDrummer or Superior Drummer - Phase issues between tracks ?

When miking and mixing live drums, you have to be aware of phase problems, canceling and comb filtering between drum mics,
 
I am just learning that and lots of advice around on it............
 
 However what about a multi-track drum sampler. I just looked at the waveform of a simple easy drummer groove. It seems to me............
 
1. The snare top and snare bottom are out of phase.
2. The individual drums are out of time with the overhead and the
3. Overhead is out of time with the room.
 
So this is what you would expect with a real miked kit... but it has never occured to me to go look at each track in EZderummer and correct the phase and timing relationships between tracks. When you go in and do it and align the waveforms, you get a mich tighter, crisper and powerful sound, but still have the room ambience to allow them to sound real.
 
So is this known ?. Is it just me ? or do I have this wrong (quite possibly)
 
Just wondering if this should be practice when using software drummers. I will ask on Toon track site but answers here are generally better.
Cheers
 
Chris.

ok, I freeze, not bounce, so I will try ...
 
Cheers