Okay.  It's just I had a similar problem on a project yesterday.
 
Twenty two tracks, two instances of EZDrummer.  Everything working fine.
 
Then inserted LP64 EQ onto lead Vocal.  All still fine.
 
Then inserted LP64 EQ on backing vocal track that already had Perfect Space on it, and half of the drums on the EZDrummer Twisted Kit Track disappeared.  Was just investigating it when I read your post.
 
The track keeps playing only part of the kit even if I turn LP64 and PS off.  If I delete either PS or LP64, everything returns to normal.
 
Just wondered if you may be using any look ahead, CPU intensive or LP plug ins.
 
Still think this is odd.

Midi buffer settings are fine.  I think something might have corrupted my Kontakt 5 when I unfroze the drum track. I did have Sonar crash.  I've been having them more these days.  Where Sonar goes into Ghost mode and doesn't respond.  I'm going to reinstall Kontakt and see if that does the trick. 

Well, re-install of Kontackt didn't do it.  I even found and update on Studio Drummer from Native Instruments.  Nada.  

 I'm pulling my hair out.  Wait!  What hair.  LOL

I've had and have the same problem with Kontact. And, just today Dim Pro. 
Sorry, I don't have a remedy. (I'm on 8.53 though).

Ok.  Here's an update.  

I just tried "Converting Midi clip to Step Sequencer and the clip plays perfectly.  So What caused this?  Hmmmm. 


The reason I'm very protective of these groove clips is that I spent so much time in tightening them up.  I was transcribing some Steve Jordan parts and copying his feel.  They were sounding so sweet with fills and dynamics.  I'm just blowing a fuse now.  

I may have to call support tomorrow.  I am not finding this solution anywhere on the forums.

I had this exact same problem with Studio Drummer in Pro Tools once.  And if you Google around you will find that others have had the same problem in other DAW's...here's someone on the NI forum complaining about skipped MIDI notes in Live, for instance. 

http://www.native-instruments.com/forum/showthread.php?t=170292

Recently had the same thing occur in 8.5.3 a few times, NI Studio drums, in Battery 2. Turns out it was a latency issue...as I kept piling plugins into the project the issue suddenly occured. In one case slightly increasing the latency solved the problem, in another increasing made it worse (it started stalling during playback) and decreasing the latency solved it. Can't hurt to try, only takes a few seconds and you can always set it back the way it was.

Thanks Sharke and SToons!! 

I can see that it's not explained well either on other posts.  I don't believe it's a latency issue.  If it were I believe the missing note plays would happen randomly.  However, through extensive testing, it only occurs on these two specific groove loops that I created.  And it misses hi-hat only in one and the kick and snare in the other.  It's a consistent fail not a random fail. 

Still searching.  Thanks gentleman. 

Try turning off all looping (including the groove clip looping) and then copying and pasting several intances of the loop. I have had issues in the past with the looping, particularly when running VSTi's. Unfortunately if that works it may be a workaround and not a solution.
 
To bad it isn't more convenient to be able to just post things like that groove clip, it would be good to see if it repeats for others. And some here might see things others like myself wouldn't.
 
As for the latency thing, in my case it was all the hats missing in one case, not just sporadic dropped notes.