Debilitating input lag

[Dimpl]

While playing Super Paper Mario, every so often I get input lag of ~400ms or stuck keys for a few seconds, and then it goes back to normal. Turning down settings did not seem to help with the issue. My FPS does not change, and the input lag occurs across my whole computer (eg. it came up every so often while I was writing this post, with SPM running minimised). What could I do to stop this happening?