Questions and Answers
Did the DM employ house rules when he had my character make a Bluff skill check when my character was telling the truth?
Yes. Officially, the Bluff skill uses are appear innocuous (Complete Adventurer 102), creating a diversion to hide (Player's Handbook 67-9), delivering a secret message (PH 67-9), disguise surface thoughts (Epic Level Handbook 39), display false alignment (EL 39), feinting in combat (PH 67-9), heckle (Races of Stone 130), "I meant to do that" (April Fools column "Fabulous Cats!"), instill suggestion (EL 39), and lying (PH 67-9).
Undoubtedly, there are more uses for the skill Bluff in other sources, but none of the above skill uses support the DM's ruling that a character makes a Bluff skill check when telling the truth.
If it isn't strictly necessary to make a Bluff skill check when telling the truth, are there circumstances when a Bluff skill check when telling the truth could be necessary?
Outside of the DM saying, "Make a Bluff skill check now," I can't think of any. The most common Bluff skill use is lying, and, while the Bluff skill can do other things, making a character who's already telling the truth seem more believable isn't a published function of the Bluff skill. (Asking the DM to quantify his house rules for what was obviously an off-the-cuff ruling is liable to lead to hard feelings, however.)
"Well, then, why'd the DM make me roll?"
The DM probably made you roll because he was in a narrative corner and needed an out. Maybe the DM was expecting you to gather more evidence before having this encounter and didn't know what to do when you hit it early. The DM, caught with his pants down, hadn't previously quantified exactly how much evidence the NPC needed as proof of your veracity, and, instead of employing any one of a variety of DM techniques that could've been more satisfying, he made you roll, even though you aren't doing anything that necessitated a roll.
"What could've the DM done?"
The NPC who posed the question could've asked you the question, and, when you told the truth, could've simply said, "You're lying." Then, upon protesting your truthfulness, the NPC could've proposed a test, a quest, or the gathering of more proof of your claim that would lead to his belief in your honesty. In other words...
Example 1
DM: (as Lord Flaconsun) Are you my son, heir to Castle Falconsun?
Player: (as Tyrone Falconsun who was reincarnated as troglodyte) Yes.
DM: Then prove it.
Player: How, father?
DM: Only my son knows the answer to this riddle: What remains in an empty pocket?
Player: A hole, father. I remember that riddle from when I was young!
DM: And what kind of tree can one carry in one's hand?
Player: You have never asked me that riddle before, father.
DM: Seek... the answer! (Ominous music.)
Player: I will seek it to reclaim my place by your side.
Example 2
DM: Are you my son, heir to Castle Falconsun?
Player: Yes.
DM: I cannot believe you. You must prove yourself a Falconsun.
Player: How, father?
DM: By defeating the Demon Dragon of Horrorspike Pass! (Ominous music.)
Player: It will be done, father!
Example 3
DM: Are you my son, heir to Castle Falconsun?
Player: Yes.
DM: Then prove it.
Player: Here is a notarized document from the Arsisus the Kind Forest Druid who reincarnated me, expressing his dismay at my new form. Here's an affidavit from King Blghrth of the troglodytes, relinquishing all claim on me as one of his subjects as my scent was unlike any he'd ever smelled. Here's the signet ring you gave me when I was 7.
DM: It is enough. Son!
Player: Father!
And if the question involved the NPC not believing you because you are the messenger rather than someone the NPC trusts, perhaps the NPC needs to hear the same information from a more reputable source that you're supposed to find. Either that, or the DM expects you to improve your reputation before returning and being posed the question again.
...But it doesn't sound like the DM had made these plans. So, instead, he made you roll, and, lacking a skill or statistic for gauging your character's sincerity, the DM had you make a Bluff skill check because, he assumed, that's close enough.
"What should've the DM done?"
I don't think--in this case--anyone should've rolled. Some things aren't up to the dice. The adventure is often gathering enough evidence, while presenting that evidence to the authorities means just hoping it's sufficiently actionable and seeing what happens. There's no roll for that part after the evidence is gathered unless one's browbeating fake witnesses, forging evidence, lying about events, or whatever.
Many games mechanize sincerity to a degree that makes me uncomfortable as DM and player (e.g. the Hero System's skill Persuasion). A character's ability to be sincere is, barring sociopathy, the character's normal state. The hypothetical special ability or skill Convince Others of the Absurd but True eliminates even more already limited NPC agency. Let the PC and the evidence do the talking and let the NPC do the deciding.
"What can I do so this doesn't happen again?"
Okay, if the DM insists on have the character make Bluff checks when telling the truth, change the goal. Instead of lawyering up when asked a question, answer the question by asking for something.
Example 3.1
DM: Are you my son, heir to Castle Falconsun?
Player: I've come for my inheritance.
DM: The effrontery of this troglodyte! Remove him!
Player: Here is a notarized document from the Arsisus the Kind Forest Druid who reincarnated me, expressing his dismay at my new form. Here's an affidavit from King Blghrth of the troglodytes, relinquishing all claim on me as one of his subjects as my scent was unlike any he'd ever smelled. Here's the signet ring you gave me when I was 7.
DM: Son!
DM: Father! And gold!
Asking for something should turn the Bluff skill check into a negotiated Diplomacy skill check. (If the character's really bold, he might attempt an Intimidate skill check instead, but given the situations in which PCs usually find themselves this is liable to be unwise.) It's entirely reasonable, for example, for the PCs to present the king with evidence of the impending orc invasion then ask to be placed in charge of an army to crush the orc forces. That second part's a Diplomacy check using the negotiation rules (PH 71-2), but that first part's just showing up with enough orc heads in a bag of holding to prove to the king the threat's for real.