There are a few contextual clues to suggest that the plant was the first life that any EVE probe has returned, period.
- The Captain notes that it's the first time in his tenure that a probe has returned positive. AUTO seems compelled to tell him, if only to turn off the warning light.
AUTOPILOT: Probe One has returned positive.
CAPTAIN: But...no probe's ever come back positive...before.
- The Operation Manual is covered with a thick layer of dust, suggesting it's been unused for centuries
- As we pan away at the end of the film, we see that the ground away from the city is literally covered in plants of the same type as the plant that Eve found. This mono-culture (and the lack of positive probes found in the Captain's tenure) would strongly imply that this kind of plant was a recent mutation that has taken hold.
But overall, you're right. There are no specific indications that other probes over the centuries haven't returned positive, and that AUTO has simply disposed of them. Let's face it, he's not exactly stable.