It's not exactly a running gag, at least not intentionally.
Things don't really get non-linear until the new series, with three exceptions. For the most part, the Doctor aged consistently from somewhere between 236 and 450, to somewhere in the high 900s during the TV series, and from there to 1012 up to the early Eighth Doctor Adventures novels, and that's consistent across pretty much all media.
So, if you only go by TV, the 9th Doctor ought to be at least 1000, and if you include everything, he ought to be more like 1800. And yet, he claims to be 900—younger than the 7th Doctor in his first adventure. Russell T Davies has never explained why. Of course you can make up in-universe explanations, but he never attempted to do so.
Paul Cornell pointed out that the 9th Doctor never actually said he was 900. He said he'd had '900 years of time and space', and '900 years of phone-box travel', and that he'd used the name 'the Doctor' for over 9 centuries. To anyone paying attention, that makes him over 1136. But the press interpreted it as the Doctor saying he was just over 900 years old. And, in the next season, the 10th Doctor confirmed that interpretation, saying he was 903, and aging from there up to 909.
It's almost as if RTD at first just said vague things to avoid dealing with the question, but then once everyone started assuming that meant '900 years old' it was just easier to pretend they were right. And in-universe, the Doctor could have done the exact same thing as RTD. In fact, Rose introduced him as over 900 before the first time he said he was 903.
Steven Moffat originally endorsed Cornell's explanation, but he later took it even farther. The reason the Doctor was being vague was that he has absolutely no idea. Any number he gives is a lie. For all he knows, he could be millions of years old. After all, as the Doctor explained to Amy, history is always contradictory for everyone all the time. Of course this, like Cornell's answer, is only his retroactive explanation for RTD's stories (and Terrance Dicks', and so on); it's only authoritative for series 5 on.
So, there are many possible answers to your question. For example:
- the Doctor's age is linear, but the events of the EDAs and/or the Last Great Time War and/or the timey-wimey nature of the post-Gallifrey universe have made a confusing mess of things, and now he no longer knows the right answer (nor do the writers).
- the Doctor's age was linear until those events, but no longer is, so there is no right answer anymore.
- the Doctor's age was never linear, and only gets worse the more he lives (and travels in time); he gamely tried to give consistent answers for a while, but eventually gave up trying.
And probably plenty of others.
- The 3rd Doctor twice claimed to be several thousand years old, before the 4th Doctor set his age at 748. This was never explained in-universe, but out-of-universe, the writers of The Discontinuity Guide suggested that the 3rd Doctor had just been exaggerating for effect, and Terrance Dicks, who'd written most of the episodes in question, jumped on that and decided it was retroactively true.
- The 4th Doctor was somewhat inconsistent. While aging from 748 to 760, he also gave ages like 747 and 730. However, he was clearly fudging his age when he could get away with it—Romana directly caught him on it once. So, he may have been a few years older than 760, but it's at least close. And none of his successors ever did anything like that—the 6th Doctor rounded down once, but he directly said he was estimating.
- After the early Eighth Doctor Adventures novels, things get very confusing. In the EDAs, the Doctor loses his memory, and then there's an orgy of history-editing, so there's somewhere between 112 and several hundred years of stories where he doesn't know his age, and there might not even be a definitive answer. Meanwhile, Big Finish started their own New Eighth Doctor Adventures audios, with over 600 years of further adventures, and deliberately avoided specifying where they fit within the EDA chronology.
- Who was certainly aware of the novels—he wrote one where the Doctor was over 1000.
- For example, given how much his history was edited in the EDA novels, it would be surprising if his age never changed.
- Since he stole the TARDIS at 236, according to "The Pirate Planet".
- At least in the post-Gallifrey universe.