Hi Lachlan,
1. The issue is likely that the pump is making a very poor seal on the tube. To fix this there are instructions in the manual for how to put some extra tape inside the pump head to make it “tighter”. Have you done this? Basically the issue arises from poor manufacturing tolerances on the pump head, so we have been using this to improve them where needed.
2. I am surprised the silver tracks did not turn it off. Generally people find these are TOO sensitive to moisture, rather than missing it entirely. Was the liquid leaking directly onto them, or somehow avoiding it? One possibility is there might be a wiring fault on that reactor. To test such a thing I would recommend starting a blank experiment (e.g. just put a test tube with some water in), press “Start” on the interface, then DELIBERATELY short the tracks with a piece of metal or other conductive item to check that indeed it crashes the software (can take up to 30 seconds or something for it to trigger).