@jimp Dude... You... are.... an... angel!!!!
I totally missed this and would never have thought of looking for this. You nailed it.
I just tried some scps just to see that uploading through the ipsec tunnel immediately failed and was suspecting my fibre provider etc. It was exactly as you suggested. Applying the patches and rebooting brought be back to a workable state and most likely will have solved my sshuttle problems as well.
I honestly cannot thank you enough! Well done mate!