This kind of thing always blows my mind. After I used flounder incorrectly at work, one of my bosses showed me the following entry in a book, 100 Words Almost Everyone Mixes Up or Mangles, that she purchased for me a few months ago. :)
Flounder, verb:1. To move clumsily or with little progress, as through water or mud.2. To act or function in a confused or directionless manner; struggle.Founder, verb:1. To sink below the surface of the water.2. To cave in, sink.3. To fail utterly, collapse.Example:"If a student is foundering in Chemistry 101, he had better drop the course; if he is floundering, he may yet pull through."
Since I didn't know that founder the verb existed until now, I definitely have been using flounder for all of those meanings!
Think about this: if a person flounders in the water, that person will likely founder at times.