Hi James,
Seems we have an audience.........
You've got the bentonite mix spot on - putty-like is exactly what you want. It went in as a slurry, hydrated and probably picked up some more water from the surroundings, and it's set off. It'll go harder if it dries out, and may even crack, but it'll heal itself and swell up when it gets wet again.
Canal is not an issue. I know roughly where you are. I'll dig out the geological maps and get back to you on those.
The clay under your house will not be a particularly good seal. It'll have lots of disturbance as a result of your house being built, and there will be brick ends etc incorporated, so it won't be particularly 'waterproof'. There may even have been some previous use of the site - you can check this on the Old Ordnance Survey websites (for free). You can go back to the 1st Ed of the OS, usually around 1850. You may have had a bleach works for example since you're here up north, or some industrial facility on your property before. That'll have disturbed the ground too so what you might think is a clay and should be a seal, in fact is riddled with discontinuities which can transmit water flow.
FWIW, when I was building landfills, even if we were sitting on metres of clay, the top metre or so came up and was replaced in layers, rolled and compacted. There's a lot of QC associated with that process. That's because there's micro-fissuring etc in the clay as a result of freeze-thaw at the end of the glaciations, and desiccation as a result of weather, and there are always inclusions of granular material in the North - so a natural clay may not be a particularly good seal. You might get away with it in the Oxford, Kimmeridge and London Clays, but no chance in the northern clays. The northern 'clays', other than the Coal Measures clays, tend not to be very good at shrink and swell too, and their clay mineral content can be low, being replaced with rock 'flour' from glacial action. Given your location, I'd not expect the local clays to be a particularly good seal, and my earlier point about water flow under the house is even more valid.
Monitoring: not easy, particularly given the 'micro' nature of 'the site'. Is there anywhere else you can get a look at the soil under the floor? If it's more of a widespread phenomenon, then that tells me it's a wider flow under the house. If other places are dry, then it's probably a confined pathway associated with that water pipe, as you expected. Don't forget, that it's laid in a trench in the clay and that pathway will have a very, very large effective permeability when compared to the surrounding clay.
Can you investigate the pipe trench further under the house, i.e away from the outside wall? I wonder if the water's coming that way rather than from the outside, i.e. the water flow direction is the reverse of what's been assumed so far. That was my pont about dye tracing, although the natural filtration effects of water passing through soil may take the dye out, so it's not a foolproof test.
This is not an easy issue to resolve - given the small size of the site in geological terms, and the limited access.
Finally, are you sure you don't have a water pipe leak? That would fill the pipe trench to the top so it overflows across the soil surface under the house - it would then pool on top of the bentonite. Got a water meter?