If you haven’t yet, best to convert all your audio elements to FCP’s favorite 48k 16 bit aiff, before adding to the sequence. This is quickly and easily done with Compressor.
If on a fresh sequence and you’re using uniformly encoded audio as spec’d above, yet things begin to act quirky make sure you have performed a Mixdown of the sequence.
It’s as simple as selecting all the audio elements on your sequence and from the menu bar choose Sequence>Render Only>Mixdown. If you change something after that, you may again hear weird playbacks. If so, trash your audio renders and Mixdown again.
Before a final export, I always trash all video and audio renders (Render Manager, under “Tools”) and render everything fresh, including a Mixdown.