I think the bottom line is SONAR, Windows, or both need to handle MP4s better. It would also help if Vegas didn't pad the beginning of the file when exporting, otherwise when exporting MP4 from Vegas and importing the same file back into Vegas (no SONAR involvement at all) the audio wouldn't be late when imported. 

How late is your mp4 to mp4 test in vegas? Mine was barely a quarter frame.
 

I am a bit confused as to why this is causing a problem.
 
Years ago I did a lot of audio for TV/Film.
 
A quick rundown of how we operated is:
I would get given the capture which contained audio captured by the camera and a separate track of the proper audio capture. 
I would line up the clapper board spikes from each in the DAW and edit the audio.
Then once the audio was processed (Some EQ, compression and volume adjustments) and any music needed was recorded (Music was done in a separate project) it was given to the editors who would place the music as they wanted it.
To fit it all back to the video they would simply align the clapper spikes on the main audio.
 
They would then render it all together - then edit that cut down to remove the clapper, do titles / credits etc etc.
Then you had the finished product. Always perfectly in sync.
 
 
The whole 'TAKE ONE SCENE ONE - CLAPP!!!' thing is just for this purpose.
To create an Audio spike in both the camera and main audio for alignment which is done during final edit.
If you are doing the audio after the final edit - then you're doing it the wrong way.
 
 
So something exporting even 2498 frames out of sync shouldn't matter if your procedures are correct.

Sorry, not sure what your posting that info for. I know how to sync up two things. It's Sonar that doesn't! LOL

Hello, we'll take a look at this. I haven't noticed any sync issues with MP4 when I tested.
Can you provide a sample MP4 file and simple project that exhibits the problem? Put it on a file share and send me a link...

Thank you Noel!! File share link below and a description of the contents:
 
Here is a link to the various test files in a zipped folder:
https://dl.dropboxusercontent.com/u/483200/sonarsynctest.zip 
 
Included:
1. Short MP4 file
2. Screen shot of Sonar's clock vs burn-in time code clock not lining up
3. Wave file of audio exported out of sonar (from the mp4s audio track)
4. New MP4 rendered in Sony Vegas 12 with both the original audio and the sonar exported audio (I panned it to the opposite side, is out of sync)
5. Screen shot of the two audio files in vegas (out of sync)
6. Platinum bundle file of the session with the mp4
 
Comments:
First off, thank you Noel for having a look at this, I know you get many issues brought to your attention.
 
- The issue does not show itself within Sonar, the issue is the audio (score in this case) exported from Sonar and brought back into other programs like: (Sony Vegas 12 or ProTools 10 HD) I've also tested with Cubase 7.
You would need a second program to test out this issue as files exported out and then back in to Sonar sync up fine.
 
When a composer scores in Sonar, obviously his or her output needs to sync back up to the sessions in the film production house. They are generally on Pro Tools as you know. The wave files exported from a Sonar session containing an MP4 or QuickTime file (I'm assuming any compressed video file) will have some sort of padding at the top so that the exported audio plays late in relation to the audio in the original MP4s timeline. I'm using dialogue from the original MP4 to test this out. I believe the encoding on this MP4 was originally H.264. I have made my own MP4 for this test just to make the file shorter but I get the same result as on the original MP4.
 
The basic test I do is this: 
- Import MP4 into sonar, set the sample rate 48 KHz, bit depth 24, frame rate 23.97 and clock offset 00:59:52:00
- Export part or all of the audio out as a wave file or better, a Broadcast wave file
- Open the same MP4 in Vegas, Pro tools or any other pro program that handles video and audio
- Import the audio that was exported from Sonar into the other program.
- The audio will be out of sync with the original. (late by 3/4 frame up to 1.5 frames depending on the Sonar version)
- * Go through the bundle's time-line a bit and you'll notice the visual code and sonar's code are off, not consistently either. This is not the same in PT or Vegas, every frame lines up.
 
* If I do these tests between the other programs (not sonar) I get sample accurate sync as I should. I think this rules out Windows, the newer MS media platform, or any other third party technology. If it works in the other programs, why not Sonar? Something is odd about the way sonar imports these compressed video files into it's video container. There is no drift and the sync issue occurs right from the start of the file and is consistent to the end of the file.
Even if I get Sonar's clock to line up with the visual code on the MP4, any exported audio will have that padding and be out of sync when I re-sync it in another program. I should also mention that I've tested this with MP4s that have different frame rates, sample rates etc. and/or no clock offset, same issue. Everyone in the business is using mp4 and QuickTime during production these days so this would be a worth while improvement. This message is too long now, if you have any other questions please let me know. Thanks again!
JG 

Sonar does seem to permit configuring a "Start time" in the video track. It allows resolution to Sonar's tick level, which can be 1/480 of a quarter note. Of course project tempo will influence the exact time. Is this something that can be used during export as a workaround to correct the offset? I'm assuming this would be more convenient than bouncing an audio track then offsetting the audio. Also I'm assuming that there is no problem with "drift" over time, just the starting offset. Also, if that offset is different in every project, that is even more of a pain.

Apparently:
"Adjusting a video clip’s start time is currently only supported when using the DirectShow video engine, not when using the Media Foundation video engine" *Thanks for the feature... that doesn't work! lol
 
I've tried simply altering the smpte clock offset to compensate among other things. I have workarounds but even with the tick resolution, it's not quite small enough to get the locked up tight. The other programs I test are SAMPLE accurate, so you can literally play two identical wave files at once and not have any phase or flange issues, it just sounds like one file playing. Sonar should be sample accurate, it is on all other levels, I think it's just something having to do with compressed video files. (currently I slide the audio 70 ticks earlier before exporting to get the closest sync possible)
 
Thanks 

Too bad about Media Foundation video engine. But about the 70 ticks, you should be able to slide the audio by samples. Of course you would need to zoom up and turn off snap.

Yes, by hand you can get in right to the sample if you zoom in and slide the file, no snap. I deal with too many clips in my score so I need a way to do it globally and consistently. So I use the slide feature set to ticks. It's pretty close. I shouldn't have to which is the things that bugs me...   
 
Not sure if it's a MF video engine thing either, I'm testing with other programs like protools and vegas without a problem. It's most likely sonar related