Lots of possibilites.....some are: when you say checking audio levels of your sequence...does that mean meters of your audio board, or meters in PrP? what are you using to monitor audio to your speakers? when outputting are you then playing back off your computer speakers? Lots of possiblilites here. Can you tell us a step by step and your configuration?
What software are you using to play back the exported file? For example with VLC you can adjust the master volume over 100% -> Distortion while the master file is ok.