Micro tonic Multi is out of sync with Ableton's clock.
This is very apparent when recording channels into audio clips.
The problem is not specific to AU or VST.
Buffer size is set at 1024.
What is the solution?

This is strange. I have not heard of anyone having problems with sync in Ableton Live before. Live also happens to be my personal DAW of choice and the one I use primarily when developing our plug-ins.

If you are not using the latest version of Live (9.2) there are some known issues with sync if you use effect plug-ins that adds latency, but this shouldn't normally affect Microtonic. This is the only known timing problem in Live that I am aware of, and it is fixed in 9.2.

Do you use Microtonic's internal sequencer or do you use MIDI clips in Live? Also, could you please provide us with some audio examples of how exactly Microtonic is sounding out of sync?