There are all sorts of things that could be factors here, but I would bet the primary (heh) factor is simply age.
First off, as you mentioned, they are different strains and *should* behave differently.
Secondly, brett as a primary fermenter (e.g. a starter) tastes very different than brett as a secondary. Tropical fruit can be a "primary" flavor for Brett C (Mike T might disagree here.. I know he's not gotten the pineapple, but I've gotten huge pineapple and mango). The Drie Fonteinen Brett B strain can also give you fruit (this is the strain sold as Brett L. by Wyeast/White Labs).
Third, brett can and often does mutate, giving different flavors at different times. Avery 15 is a great example of this.
Fourth, the flavors you get from brett will depend in part on what flavor compounds already exist and in what conditions you use it. For example, brett changes lactic acid into ethyl lactate, tends to metabolize "clove" phenols, and so on. You should expect starter worts to taste quite different than a mature beer with a brett secondary.
Edit: Fixed a couple things.
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