Sonar X3 - No audio from Kontakt after playback pause and resume

Is it possible that your setting of 'Reset All Controllers to Zero' might be taking volume down for these particular instruments?
 
Every once in a while, I run across the above issue, and have to turn that parameter off for things to work properly.
 
The construction/implementation of some individual instruments within a given plugin, as well as certain plugins in their entirety, can have strange reliance for some parameters built into connections with standard controllers, so when Sonar resets these, it can cause some plugins or certain instruments within a plugin, to behave strangely, like what you are experiencing.
 
No guarantee the above is what is causing your issues - but it is something you can check out real quick in Preferences.
 
I have a completely separate thing for you to remember, with regard to Kontakt 5, and some other NI synths.  Some of them are set to react to a fader volume change by adjusting the main output volume for the synth, but there is some weirdness in how that is implemented.
 
Sonar will give you a default midi volume set at 100 or 101, for the setting on a midi track's fader.  If you drop that down to some lower level, then later on you go into the UI for the synth and change the master output volume there for the synth, then hit Play - you may find that the synth will jump back to some lower volume level, all on its own, as soon as you hit play.
 
It seems to be tied to that fader setting, so when the fader volume was lowered, even though you raised the output volume in the synth, hitting Play caused it to jump to the level that was set by the fader volume level.
 
I know that for Battery 3, there is a setting in its Options that you can turn that behavior off/on.  I have its default behavior for that turned off.  
 
I suggest at some point you take a few minutes and look at that behavior, so that you don't go crazy later, trying to figure out why it is HAUNTED.  :)
 
Bob Bone