I currently have this issue on my modded KSP 1.3.1 install, here's my mod list, perhaps we can compare our installed mods to narrow down the culprit.
Also, I have seen this issue before, it was caused by CKAN not installing the mod correctly.
Edit: Having looked in the gamedata folder, it seems (in my case at least) that the culprit is control-surface-toggle again.
Edit2: nope, uninstalled it and still have the issue.