OS? What changed? Have you rebooted?
Changes can include anti-virus updates, new movie players, downloaded apps from the internet. There's not much to go on in your description. Compressed audio should not be used in production, try wav at 16 bit and 48 KHZ (video standard). Try a completely new comp with nothing in it but a wav file or an aiff file.
No I have not rebooted but I haven't done anything. No downloads and hardly any internet browsing.
So wav files are the ones I should be using? I read somewhere that AIFF is the best for AE. Otherwise would the m4a be just as good as a wav?
AE sucks at any compressed audio format. AIFF is okay, but on a Windows system one would use straight WAVs most of the time. Your issue is probably reltaed to caching the audio files, so check your settings for the media cache and flush it if necessary.