Flintas |
I'd say it would depend where the alternate movement type comes from.
If it's a natural racial movement I'd say yes.
If it's from a template or class ability, such as the fly speed of a half-dragon, then I'd say you use your modified base speed to determine the alternate movement speed.
If it's from a source such as a spell or magic item, I'd say no as these would not be your base speed. Unless the spell says it's based on or affected by your base speed.