I noted this earlier in the thread - it doesn't say "a spell with an instantaneous duration can’t be dispelled" - it says rather "the effect of a spell...". In the very next clause, they explain that this due to the the timing of the spell, which is what I've been saying all along. Instantaneous duration in no way implies that a spell is non-dispellable, only that the effect of the spell, which remains after the spell has terminated, is non-dispellable. You can't dispel the charring left by a Fireball spell, and similarly you can't dispel the petrification left by Flesh to Stone.
Your interpretation only holds if "effect of the spell" and "spell" mean exactly the same thing, which they obviously don't, and if the spell description of BE is self contradictory. My interpretation has "effect of the spell" referring, quite logically, to the effect of the spell, and it has the description of BE making perfect sense. Your interpretation thus requires two statements in the rules to be absurd, while mine does not, therefore logic suggests that my interpretation is more likely to be the correct one.
The reason Stone to Flesh is there at all, aside from simple historical reasons, is probably because BE apparently doesn't function with all petrification effects. I wasn't sure about that at first, but now that I look at the 3.5 StoF description
alongside the BE description
it seems probable that they intended for BE not to work with forms of petrification that aren't explicitly transmutation spell effects. StoF of course also is renowned as the really gross way of getting past a stone wall...
