williamcopper
And I'd scour this forum for posts like this one.
Unfortunately no one from Cakewalk could benefit from the information you provided in this thread. There is virtually no information on which anyone can act - no data on how to reproduce, no indication of the exact nature of the project, whether you used multiple single instances of Kontakt or multiple instruments within a single instance of Kontakt, whether there was scripting involved in the Kontakt programs, etc. etc.
It's all well and good to follow false trails...but it's probably better not to ask people to follow you on your false trails until you can present at least somewhat more substantive information than a couple sentences and screen shot from another program, which you apparently don't know very well if don't know how to invert phase - so there's another variable. (FYI you can invert the right and/or left channels in the Object Editor. Or select the object and choose Invert Phase for either or both channels from the Real Time effects.)
What you've presented contradicts
all the experiences I've had with multiple projects over several years that involved rendering and bouncing. Therefore if I've never encountered the issue and you can't provide a method to reproduce, I don't find your information particularly compelling. Nor do I understand why you brought the files into Samplitude. Once the MIDI has been converted to audio,
it's audio and a start time differential would show up in any program, including SONAR. Maybe you exported the audio outside of SONAR...who knows...
Those whose motivation is
improving the program and who cannot provide steps to reproduce send projects to Cakewalk so that they can be analyzed. Cakewalk has an extensive collection of programs, including Kontakt, with which they do extensive testing because it's a popular instrument among SONAR users.