I can't help you directly about Canada, but I have a Bike Friday folding bike that has been to Europe a dozen times and I've never had a problem on re-entry to the US (or entry in to the UK or Germany).

That being said, I do always clean the bike before packing, remove all obvious dirt. A friend has an S&S coupled mountain bike and he did receive some hassle once as his bike was fairly mud spattered. People's hiking boots probably have more chance of soil contamination that your Brompton's tires