Normalizing and filtering out DC offset won’t always fix this “crunching” issue you’re facing.
While it’s certainly possibly I’m inclined to say it’s not the cables, given how this issue is only at one portion, and this only seems to happen when there’s one passage of lots of low frequency info (bass and kick seem to trigger it) during other already somewhat louder passages.
Do you have automatic gain control turned on? It could have raised your levels for you during a quieter passage then not backed them off during this louder portion, causing the limiters to kick in and brickwalling your recording.
On an unrelated note, glad to see you’re getting usage out of my old DR-40! Seems you’re using it more than I did.