Generally, in these situations you have a choice:
1) Just change the population to something higher. This is really the best idea; it's the fastest, explains the results the best, and requires the fewest changes. In Traveller's long history, everyone knows the stupid results of randomly generated systems. It's part of what makes Traveller a joke among many RPG players. Grognards wave their rulebooks in their long grey beards and frock coats and claim we have to explain it away, but that just gets old after the 10th time of seeing these stupid results. The canon police aren't going to break down your door for changing this.
2) However, if the novelty explaining these idiotic results that random die rolls produce still hasn't gotten old to you, I have a few ideas:
* In the case of a habitable planet like you describe there, I'd steer away from any cause that can be overcome by technology: Things like incompatible biology (such as diseases, hostile animals, etc.), the ever-popular "inexplicable radiation", and causes like that. It's in a nice position, people would settle there and the 3I's technology could overcome things like this. At least, it shouldn't be the only reason why nobody lives there.
* The most likely cause is political. It's not that nobody chooses to settle it, it's that it is illegal to settle there for some reason. Another reason might be some wonky tradition or something.
The name of the world is very evocative, so I'd work with that somehow. Population 1 is like 1-100 people as registered citizens of the world. So here we go:
At some point, this world was settled by settlers in something like a sublight sleeper ship or a generation ship or something similar, launched from Earth Way Back When (tm). Or perhaps it was a similar project during the Long Night. They landed on the world and they named their world Our Planet. However, their technology never really improved that much and in fact it backslid to like like TL1 or something over the years due to conditions on the world that the settlers were unsuited to cope with before rebuilding in population again.
Hundreds of years pass.
Eventually the area of space becomes the frontier of the 3I. In the wild and wooly days of the beginning of settlement and exploration of the area, a lot of worlds were settled. This world was no different. It was a pretty nice world, after all. By this time, the population of the world was in some millions of low tech natives. Naturally, higher-tech settlers simply landed and settled the world, too. The natives were responded to as they reacted: If they resisted or were in the way, they were killed or driven off. If they were not, they were ignored. If they approached relatively peacefully they were allowed to live in shanties or whatever and work menial jobs for the new settlers.
However, the problem was that there was quite a bit of resources on the world. Nice ones, useful for higher-order TL12+ industries. As the worlds in the area began to reach these TLs, hungry eyes turned to the world. They began make arrangements with various settler groups on the worlds. Rivalries between the groups on world and their backers led to a long and bitter war. Eventually nuclear weapons were used; they didn't wreck the world's ecology or anything, but they certainly got the attention of the Imperium. The Imperial Navy and Marines showed up to try and make sense of the situation and deal with it. With so many imperial nobles (and powerful ones) with a vested interest on the world, the problem kept getting escalated up the Imperial chain of nobility until it finally reached the ear of the Emperor.
The Emperor, who obviously has a lot more on his or her mind that dealing with some small planet on the frontier simply took a quick glance over the situation and declared, "if outsiders have caused the problems with their meddling, then only the original settlers should be allowed to live on the world. Everyone else should leave."
When the Imperial bureaucracy sets about implemented the Emperor's order, they realize that the people they thought were the settlers on the world actually weren't. In fact, the original settlers of the world, most of whom have intermarried with the local population or simply died are difficult to find. However, in some remote corner of the world, they do find a tiny tribe of the pureblooded descendants of the original settlers, driven there by the later settlers. As the greater Imperium (and the Emperor) are pretty disgusted with how the entire situation was handled, they get vindictive by interpreting the Emperor's declaration literally.
Everyone who isn't that tiny tribe is no longer a citizen of the world.
Now you can go a few ways with this:
1) Literally everyone is moved off. There's only less than a hundred people on the world now.
2) Most everyone still lives there, but by this ancient technicality, they are no longer considered "citizens of the world." The tiny tribe are the only ones who are counted for voting and government of the world. Of course, they're all now fabulously rich and may govern their world well, badly, or somewhere inbetween. Perhaps each member of the tribe now is a Prince or a Princess. They hold the right to deport any of the "stateless persons" who live on the world at any time, for any reason (a right they may or may not use depending - if you're going to for Star Trek ridiculousness they probably would exercise this right, if you're going for a more "realistic" Imperium, they probably wouldn't though it's something everyone likes to joke about). Regardless, because of this technicality, while the actual population of the world is in the millions or billions or whatever, only the original tribe's members are counted as actual citizens of the world (in the years since, the original tribe has grown quite a bit, so only the inheriting heirs or something are considered citizens of the world).
3) Some exotic solution between the two. Perhaps taking the Emperor's decree literally, most of the later settlers have moved off the world and live in luxurious high-tech habitats in close orbit, taking anti-gravity shuttles anytime they have business on the world. A significant portion of the people might commute to work every day like this. Another place would be the sprawling hundreds square kilometer starport downport of the world, which with the agreement of the tribe, has an extraterritoriality status. It's a glittering TL14 walled metropolis and everyone who isn't one of the 100 (or less) citizens of the world makes their home there because again, it's technically not part of the world. Of course they might take "business trips" that last for years or decades on the world itself, but each and every non-original-settler is required to have a legal residence in the downport.
While the situation might seem strange or oppressive, perhaps the decision was made some centuries ago now, and everyone has gotten used to the situation and nobody minds it. Perhaps the original tribe are the "citizen-electors" of the world - and have long since assimilated into the population and "the thirty" is some elected body or something who govern the world by consensus - most people take perverse pride in being "resident aliens" of the world and it's just some quaint local tradition. Though I think it'd be more interesting if the tribe's descedants still hold vast power and you have to step carefully around them - fortunately, most of them are pretty reasonable people so it's no problem ... but there's always a few bad apples.
