1.If you have placed your audio on the timeline, make sure you put everything to stream.
export a large project
2.Make sure your computer has a lot of processing power: playing and recording at the same time requires a lot of RAM/CPU, look for idle processes and shut them down.
3.If nothing helps, record Audio/Video seperately and match them afterwards in AfterEffects/Premiere
4.Flash has a maximum amount of frames it can handle (16000 := 10 Minutes), if your project is getting near to that limit, try dividing your project.