Thanks for these suggestions.
I can’t see (or hear) anything wrong with the source audio.
I don’t think it’s a defragmentation issue – the first thing I tried was to defrag the disk the files are on, and this did not solve the problem. Not only that, but the glitches come in the same place every time I render the files – if it was a fragmentation issue, I’d have expected the glitches to move about, depending on where the files were being written onto the disk.
Additionally, there are no changes / key frames etc. in the AE file at the points where the glitches occur.
I’ve tried exporting just the audio as a .wav file, and looking at the file in Audition. It looks as if AE has lost one or more frame’s worth of audio at the point of the glitch – but I still don’t know why. More importantly, I don’t know how to fix it.
With best wishes