Now, I'm not talking about IP's here. But Muscle Augmentation and Muscle Toner to increase Strength and Agility do nothing to increase your base physical movement speed? Shouldn't you run/walk faster?

it does. Remember the rolls you make for sprinting? You would use your increased attributes, which would make you faster.

Stronger and more agile people don't normally "walk" faster than anyone else, and I'm pretty sure I can walk pretty damn fast if/when I wanted to despite not being an Olympic-class athlete. Running and sprinting, however, includes a Strength + Running (or Strength -1) Test. Agility doesn't play much into it; that's used more for maneuvering than outright running.

Ah, good.