[MysticCat]

Doesn't Dumbledore acknowledge, at the end of the book when he tells Harry everything, that he sent the howler? Or does Harry just say "so you sent the howler" and Dumbledore doesn't say anything?

I figure Harry doesn't recognize the voice because (1) he's still tired and stressed from fighting dementors, (2) he's tired and stressed because of being expelled from Hogwarts and then suspended with the possibility of expulsion, (3) he wasn't expecting to hear from Dumbledore and was distracted by surprise that the howler was addressed to Aunt Petunia, and (4) there is an anger/urgency in the voice that Harry isn't used to hearing.

As for altering his voice, I wondered if he used a charm so that his voice wouldn't sound the same to Harry, so as not to risk setting up the Dumbledore/Harry/Voldemort connection.

Interestingly, what Aunt Petunia tells Harry after the howler is exactly what Sirius and A. Weasley said -- don't leave the house. The way she says it sounds a little more punishing (like "you're grounded," and Harry interprets Sirius's and A. Weasley's letters as scolding), but reading it again I had to wonder if she was using that tone of voice to cover up the fact that she was looking out for Harry's safety. Remember that the other thing we are told is that she seems to understand the implications of Voldemort being "back."