But founder comes from the different etymology that gives us words like foundation, so would imply a ship tending to sink rather than merely floundering around out of control on the surface, so I would argue this was legitimate discrimination of meaning if the boat wasn’t sinking. However, I expect in practice it may have been a malaprop – see the usage note below.

1. To proceed or perform in an unsteady, faltering manner : blunder, bumble1, bungle, fudge, fumble, limp, muddle, shuffle, stagger, stumble.
To move about in an indolent or clumsy manner : wallow, welter

USAGE NOTE The verbs founder and flounder are often confused. Founder comes from a Latin word meaning “bottom” (as in foundation) and originally referred to knocking enemies down; it is now also used to mean “to fail utterly, collapse.” Flounder means “to move clumsily, thrash about,” and hence “to proceed in confusion.” If John is foundering in Chemistry 1, he had better drop the course; if he is floundering, he may yet pull through.

Roget's II: The New Thesaurus, Third Edition by the Editors of the American Heritage® Dictionary Copyright © 1995 by Houghton Mifflin Company. All rights reserved.