Hey. Had a similar problem once or twice, but mostly my own fault. My issue was a playback rate to record rate problem. I've also experienced issues with playback when using effects that throw one track out of sync, leaving the others just fine.
Remember that most DAW's handle this by feeding audio into a memory intensive algorithm that lines everything up. Audition has an output send for each track that will send output after processing changes, which gets put into the stream clock, without any regard for where the stream is currently. Audio with no effects or changes is instantly sent, audio with effects can lag slightly or greatly, depending on how intensive the effects are. The upside is that audition isn't as memory hoggish as most DAW's, and has instant playback availabile without buffering, the downside is that you have to be more responsible for your effects and the lag they cause. During final print, the audio track and stream are kept in sync, as each track is processed by sample. Each sample is sent through the effects before reaching the final output mix, then the final combined sample is added to the file. Printing and playback are vastly different processes.
First and foremost:
If they were recorded together in sync, they are in sync, even if they don't sound like it during playback. The reason is that they are each on their own playback track, which sends audio out as soon as it's processed by any added track effects. If an effect causes any lag on a track, it will sound out of sync, but never actually BE out of sync. If you experience this problem and the plugs and effects are not marked in red on the effects rack (indicating lag with that plug), you can try and print the track that lags first. You can cycle the plugins and find out which one causes lag. You can also check pre\post fader properties as these occasionally cause lag with some plugs.
Remember that after about 4-5 devices in a conventional hardware rack, there is a slight lag in audio, requiring a delay on any FOH monitors. The same is actually true of Audition as well! Some systems actually lag at 3 plugs.
Print track method:
Do a mixdown of the entire session from file menu, but in the box that appears, you'll find a section that lists "Master" as the outputted track. You can change this!! You can print the lagging track by selecting the button and putting a checkmark in the box for that track only, removing all other checkmarks. Click ok\export. When this finishes, you can place the file on a new audio track, mute the original and see how it sounds. This only works if you only need to process the track once.
You could use the cycle method to check the plugins first, then apply the plugin with the next method I'm about to explain. That would allow you to avoid the lag. First, find the offending plugin, then turn it off and print the track. Mute the original track, and place the new print on it's own track. Bus the new track out to a matching bus track by it's master out, set up busses for all other tracks too, and apply your plugin to all of them, saving a "ZERO EFFECT" profile that allows you to leave the plug on but have it equate or process to no actual effect on the audio for tracks that don't need any. Follow the method below to do this. Then adjust only the bus of the printed track and you shouldn't have any lag to worry about.
Bus tracking method
For every track, use the sends, and bus each track to a new bus for every effect. Essentially, you can use the main out for the track to go to effect 1, then bus that bus using it's main output to effect 2. The pathway for each set of audio should be the same. I've seen this done with hardware to ensure a cleaner and better sync'ed output. This method is just the digital rep of that. Even if you don't use the plug on that audio, you have to have a bus for the audio track that matches, and you have to have the plug on. Here's how you keep it out of the way: set the effect of the plug to zero (in other words adjust the settings so there is no discernible effect, or if you can set it by wet\dry, set dry to 100 and wet to 1%, forcing a processing of the audio to match for lag). Now that they all follow the same path, they should stay in sync when you play them back.
I've been using bus tracking for a while now. Audition makes it fairly easy to do. I start with a set of about 40 tracks when mixing. Each track I record gets a set of busses, each buss gets one or two effects, depending on which computer I'm on (faster gets 2), all plugs start at a Zero Out profile, and I rarely have a problem with lag sounding out of sync. Do they lag? YES. ALL THE TRACKS LAG, so they stay in sync. Forcing lag to maintain sync is a bit convoluted but it works. I can add effects to a set of busses that are zeroed out, dupelicate the bus, send other busses, and then send the last to a master.
For my purposes one mix is never enough, as I often record live events and need audio for CD audio, audio for DVD\Blu-Ray movie, audio for youtube output. How do I get all of it at once? I record the standard recording, then add sets of mics for extra effect of the room etc, and mute them at the board I record with. I can then mix everything as I wish to get the best sound for each mix. The cool part? I can use busses to get MONO, STEREO and SURROUND. Before these master busses, I have MIX PLACEMENT busses for each recorded track. Essentially, the last effect buss uses sends to output to the placement busses, and the placement busses send to their equivalent master buss. I leave the masters muted unless I need them, and feed them out to whatever master device I want. Using the export audio tool, I almost never export a mix through the master track. I export the master busses.
For video, I often find that switching the type of audio for some input sounds better. Essentially, I create a mono mix that's selectable by menu, and a stereo\surround encoded mix that will change modes according to the settings you select in the menu. I only ever create one real mix, but I can check mono compatibility, surround\multichannel, and stereo by switching between busses. If I use an output capbable board, I can out each to a different output and just push a button or two to switch between them.
Audition's controls and nuances may seem overwhelming at first, but they are easy enough to get used to.
Awfully sorry for such a long post, but that's everything I've got. I hope it's helpful.
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