0ne thing I can come up with would be software/hardware incompatability after humanity switches to optical computers or something. But that's very thing too.
Another thing might be data scrambling. It has deteriorated beyond copy recovery to new IT systems after all those Planet years in the open away from maintenance. So discoverers have to do with what's left and still readable at the moment of discovery.
But that would still be a one-time mission. Go there, retrieve the still available data, and leave. Nothing that requires a permanent settlement.
It can always be that, before the DNA of a particular organic resource is mapped and understood, this resource has adapted to this specific spot on Planet alone. It's a niche resource so to speak, and spreading it to other places on Planet let this resource mutate in such a way that the specific thingie in that resource which kindled interest in it doesn't come up.
The ecological niche makes sense for native Chiron organisms, but as far as I can see not for terran organisms beyond the level of I assume bacteria. Complex organisms like eg banana trees most likely wouldn't be able to mutate to Chiron conditions without human intervention.
Oh, that's an easy one! The uniqueness of the contents of the pod cache makes it so valuable, a 'resource' so to speak. Sure the contents can be copied and distributed for the entertainment of the populace at large, but the real marble is owning the original stuff for your musea or somesuch. The 'happiness' is this case would be patriotism or proudness, not knowing the contents of it.
Sounds a good enough explanation for the problem of only having one resource

but not an answer to the question why you can't move the resource, which seems a critical element of the resource system to me*. For books you could say that the unity pod contained more than just a few books, rather a small library and too many for a small recon party to carry back, and that the books are too detoriated to move. But that doesn't work for movies.
* I'd say resources add three things to the game:
1) makes exploration more interesting
2) gives some interesting targets for your colonization and war efforts. This element would disappear if you could move most resources.
3) gives some stuff to trade with other factions => makes diplomacy more interesting/contentful.
Some overview of issues:
Native organisms: no problems here at all. The reason of them only living in an ecological niche can be used here to explain scarcity.
Raw materials: problem here is that they need to be rare enough to count as a resource. So stuff like iron, silicon and aluminium is out I assume. That leaves Silver and Gold which aren't in yet. A couple other elements were mentioned in this thread. Gotta check if their occurence is rare or concentrated enough. Btw, IIRC copper is pretty rare too, right?
GeoModder, in an
earlier post in this thread you mentioned silver and gold as crucial for a technological society. Why is this? For the jewely reasons, or are there others?
paper book Library cache from unity pod or wreckage: no problems
Reason for scarcity: factional pride for ownership
Reason for immobility: too many to carry for a recon party, detoriated
But then this item wouldn't be tradeable
Old Earth movies: problem with explaining immobility
Reason for scarcity: factional pride for ownership
Immobility issue: perhaps movies could be a unit that can be brought back to your cities and there turned into a building which provides some movie resources? I assume if the mechanic isn't used too frequently, it could be good.
A still functioning hydroponics pod containing some living terran plants:
Reason for immobility: too fragile to move
Reason for scarcity: prior to Cloning some reasons could be invented to explaning it being impossible to grow. Eg the tree species having gender. The found specimen is male, but no female exists anymore. But then this item wouldn't be tradeable prior to Cloning. And what after Cloning?? Then it wouldn't be scarce enough anymore to count as a resource.
Live animals:
Problems: are mobile, aren't scarce because can be bred, if not before Cloning then certainly after.
DNA data: problems: is mobile and once obtained not scarce.