I've refactored the methods used to sync the audio and midi. In certain circumstances the very first note would not be in sync with the music. I made it better at one point, and it worked in all my test scenarios, but then I started another project and it reared its ugly head again.
The problem was still with the method that primes the audio. The current process to prime the audio is to: mute the audio, play it, then in a co routine loop until the time changes. Once that happens, break out of the loop, stop the audio, unmute, then play it again along with the midi clips. This fixed this issue for the most part.
To fix it completely, I had to remove the "stop" part of the process. Now it is: mute audio, play audio, loop until the time changes, set time to 0.0, unmute audio, play audio delayed.
Look forward to seeing this in the coming update!