Freezing the track produces the same result.

Is this a simple instrument track or split Midi/Audio?

If SIT, try splitting and see what happens

are you automating the nrpns or the midi ccs? is the automation on the midi track or the synth audio output?? are you hearing the automation changes when you play back before you bounce?
My GUESS right now is that your automation is getting confused in the midi routing.  The one solution i've found for this is to explicitly define the channel in the track inspector.  to do this, select your midi track then open up track inspector. on the left you will see three drop down selectors labeled "C" "B" and "P". click on the C one and select the midi channel that track should be running to.  give that a shot.

All I'm doing is automating CC11 in a MIDI track, there is no audio in the entire cwp. The channels are assigned correctly in the inspector:
C 1 Kontakt 4 and C 2 Kontakt 4. The tracks play back correctly before bouncing. I have been doing this for 20 years and never come across something like this.

I understand there's no audio - but what is the Midi track driving? A soft synth or are you routing a hardware synth in?

If it's a soft synth, I ask again - is it a Simple Instrument Track or split Midi / Audio.

The MIDI track is driving a softsynth, Kontakt 4, it is a simple instrument track.

Right.

Split it.

Right click the synth icon next to the track number indicator and select "Split Instrument Track"

Now, what sort of automation curves have you written and which track do they appear on?

aha! well, that's the problem. with kontakt, when you map a midi cc number it does not differentiate between channels.  so, if you have say sax section in channel one and trombone section in channel two if you map midi cc 11 to "sound" on the sax section and the trombone section, kontakt only maps the cc number without distinction in channel. so, when you run automation on both it gets confused and doesn't know how to handle it.  what has to happen is map the parameter you want to control to a nrpn host automation number, and the other parameter to a diff nrpn number,  assign the automation envelopes accordingly by selecting nrpn instead of midi in the automation.  a bit confusing, i know, but because kontakt does not make differentiations between channel numbers in automation, it is the only way to do it.  as an example, i inserted sax section and trombone section.  for sax section i clicked on auto/host automation and dragged host par 11 to the sound knob.  on the trombone section i did the same thing only dragging host par 12 to the sound section.  then for each midi track i inserted automation/midi/NRPN 011 and 012 to the appropriate settings.  

hope this helps! cheers.

Thanks swamptooth and  Bristol_Jonesey.
Right clicking on the icon does not give me the option to "Split Instrument Track".
If Kontakt does not make differentiations between channel numbers in automation, how can it play the mix correctly - with automation - before the bounce?
Thanks for the workaround, that's not really a practical solution for daily work.

ive found it more than practical (then again 20 years ago i thought it was fun to use power tools for control voltage in moog modulars ;D). the only way kontakt will play back cc number automation of the same cc number doing different things in different patches is if you have the nkis in an instrument bank. because any time you open kontakt and look at the assignments for midi automation there is no setting to split channel for a cc number.  

so i guess i'm confused now.  
you have kontakt on a simple instrument track. you have more than one instrument inserted into kontakt. you have midi cc#11 controlling multiple parameters on each instrument in kontakt - one on channel one and one on channel 2.  you have two automation curves on the simple instrument track - one mapped to cc11 on channel 1 and another mapped to cc11 on channel 2. the automation envelopes for each contain different data, nodes and slopes.  if that's incorrect let me know. is there any way you can provide a screenshot??

so i'm curious now about how you assigned the midi ccs to kontakt... did you midi learn them??