Even though you'd think they can't pick up parasites somehow they manage to do it. Sometimes they carry a very slight load when you first get them but don't show any signs of it. As time goes by the parasites spread then you start to see problems.
When I see a poop change out of the blue when nothing in the diet has changed then it keeps happening, my first inclination is to take a sample to the vet for testing.
Most vets will run a fecal for you without having to see the animal first so it doesn't cost all that much. Then if they find parasites they'll want you to bring the animal in.
Runny poop isn't a good thing in any animal so that's what I'd try first then if no parasites are found, if it were my tortoise I'd go ahead & make an appointment if this keeps happening.
Let us know what happens & good luck too. 
-----
PHRatz