karhide
If you change the Sound Canvas instrument for the drums to a sound that is not drums and export does the issue still happen?

Yes.  I changed ch.10 to ch.1 (Piano), with the same result.  Count-in sounds like full velocity, the rest of the track is normal.
 
 
The count-in for most of my tracks uses a drum stick sound, velocity set to 40.  This works perfectly when played as .cwp files directly from SONAR/CbB during live performances (yeah I know, not the best thing to do, but it is what it is).
I have found that when I export the song to .wav, I need to lower the velocity of the count-in, but *only* the count-in.  The rest of the song is fine.  And that's just totally weird to me.  No idea why this happens, but at least I know that changing the count-in velocity works.
 
 

Have you shared the midi file with anyone else to test?
 

I play in a trio and use backing tracks mastered in Sonar which I then export as WAVs for use in an iPod played through the PA. I have count ins at the start of each.
I make each mix in Sonar by bouncing the tracks down to a 'Mix' track.  I then solo and Master that track using Ozone 8 in its FX bin.  I bounce that Mix track down to a 'Master' track. I solo that track and listen to it, checking it and ensuring it seems about the same level as all our other songs.  I usually tweak the count in bars as the Mastering process will have increased their volume, so I simply highlight those and use the gain adjuster in the Control bar, lowering their volume by 1,2 or 3 db as necessary.

Just a thought....

Are you running a compressor or limiter that might affect the count in? For example, on the master bus. If so that might be the cause of the problem.

Skyline_UK
I play in a trio and use backing tracks mastered in Sonar which I then export as WAVs for use in an iPod played through the PA. I have count ins at the start of each.
I make each mix in Sonar by bouncing the tracks down to a 'Mix' track.  I then solo and Master that track using Ozone 8 in its FX bin.  I bounce that Mix track down to a 'Master' track. I solo that track and listen to it, checking it and ensuring it seems about the same level as all our other songs.  I usually tweak the count in bars as the Mastering process will have increased their volume, so I simply highlight those and use the gain adjuster in the Control bar, lowering their volume by 1,2 or 3 db as necessary.

 
This is very similar to what I do. I never saw any point in not pre mixing my tracks. Once you have a "Band" that you use and come to terms with how each instrument sits in a stereo mix there seems no point in playing a multi track audio  or midi song live. 
 
I use the same Bass ( Ample)  and a custom drum kit (AD2)  for every song. Only things that are different after that are Piano, organ and the odd other instruments. 
For the bass and drums the velocity is always kept very close to my standard I've been using for 30 years. 
 
I export these mixes and then open them in Wave Lab to Master. 
First thing I do is see what the Peak level is. It should be 0.4 Db. If it is not, then something was not going through the Master bus and the Brickwall limiter. 
Then I  use the Global analyzer to see what the Average RMS level is. I want it to be around -14db and it usually is. 
Now I look at the intro and cut away any silence to leave about half second. 
I look and listen to the count in and adjust the level if need be which is rare. 
I then look at the end and cut away all silence. I like short fades so I can start the next song. 
 
When done all my songs are proofed through the PA system and it's very rare that I need to go back and adjust. 
I just re did over 100 songs using a new improved "Band" and this is by far the best tracks I ever made. I made one change where I have split the Bass out to the Left side and put everything else right. Every room is a little different so it's nice to have  more control of the low end.