I'll bet this isn't an Illustrator RGB/CMYK issue, but it doesn't hurt to mention it.
If things don't get better by turning both multiprocessing and Open GL off...
or by previewing only on the computer monitor if you have a Kona/Blackmagic/Matrox card...
try importing the project file in question into a new project.
I time stuff out to audio all the time. A good way to do it is to turn on the caps lock so the video doesn't update, and scrubbing audio. You can place markers right on the audio layers by highlighting them and hitting the * key on the numeric keypad. You can even annotate markers by double-clicking on them and adding text.
Which version are the AI files are being used and what do they actually contain? There are and always have been gigazillion issues with Illustrator files and some of them can be explained when using files from different versions and specific AI features...
I'm using AI CS5. All files are RGB and 1920 x 1080. Straight vector illustrations with solid color fill, no effects or active text.
I've tried reducing the project to one comp only and importing into another project. Same.