Shadowplay Footage Import to iMovie Introduces Audio Artifacts
After some more digging around and reading on various forums it seems that this is actually a very common problem (along with other effects, not just audio artifacts) with recordings produced by Shadowplay and subsequently imported to many editors.

It seems the source of the problem is that all files produced with Shadowplay record using variable frame rates.

There is a discussion here and here that might be useful.

There is a Handbrake preset here to convert your Shadowplay files to CFR files with no compression.

Or alternatively you can stop using shadowplay completely, skip and transcoding steps and instead use OBS Studio (free) to record your footage.