It is possible for yeast to mutate over generations, but according to my reading it usually requires > 10 generations before mutations become likely. I don't think mutations are related to what you feed the yeast (at least in terms of wort), but I don't really have any idea. Perhaps eolle is reading.
I would lean more towards your ingredients if they've changed. Also, did you keep data wrt efficiency, OG, and FG? Any changes there would affect the final product.
One other thought that occurs, if you're not 'washing' the yeast, but just scooping up trub, you are probably getting some hop residue and other precipitates that some people feel could affect your next batch. I've always washed, so I don't have any empirical data wrt that theory.