it sounds as though you are changing the global sampling rate for the project which will mess up your timing as all of your audio files are clocked at 48kHz. If you wanted to change your global sampling rate, you would have to convert all of your internal audio files used within the project to 44.1kHz too.
Is there anywhere you can upload an example of a distorted file? Have you tried exporting as 24bit, wav, aiff, high res mp3 even? With and without dithering?
It might help if you bullet point your exact steps because it really is hard to decipher what you are doing at the moment, never mind where something is going wrong!